Index

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

A - Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData

abort - Variable in class net.sf.basedb.clients.web.fileupload.FileUploadProgress

ABORT - Static variable in class net.sf.basedb.core.signal.Signal

The ABORT signal, that requests that the receiver should clean up and die.

ABORTING - Enum constant in enum class net.sf.basedb.core.Job.Status

The Signal.ABORT signal has been sent to the job, but it has not yet responded.

about - Variable in class net.sf.basedb.util.extensions.ExtensionBean

about - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile

about - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtension

about - Variable in class net.sf.basedb.util.extensions.xml.PluginInfo

About - Interface in net.sf.basedb.core.plugin

Get information, such as the name, version and authors, about a plugin.

AboutBean - Class in net.sf.basedb.util.extensions

An implementation of the About interface, which complements all getter methods with setter methods.

AboutBean() - Constructor for class net.sf.basedb.util.extensions.AboutBean

Create a new empty about instance.

AboutImpl - Class in net.sf.basedb.core.plugin

A simple implementation of the About interface.

AboutImpl(String, String, String, String, String, String, String) - Constructor for class net.sf.basedb.core.plugin.AboutImpl

Create a new about object without any min or max BASE version requirement.

AboutImpl(String, String, String, String, String, String, String, String, String) - Constructor for class net.sf.basedb.core.plugin.AboutImpl

Create a new About object.

abs(String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine

Return ABS(<value>).

abs(String) - Method in interface net.sf.basedb.core.dbengine.DbEngine

Get the function call that takes the absolute of a value.

abs(Expression) - Static method in class net.sf.basedb.core.query.Expressions

Calculate the absolute value of an expression: new expression = abs(e).

AbsConverter - Class in net.sf.basedb.util.jep.convert

Convert Abs function to a Query API Expression.

AbsConverter() - Constructor for class net.sf.basedb.util.jep.convert.AbsConverter

AbsExpression - Class in net.sf.basedb.core.query

Calculate the absolute value of an expression: abs(e).

AbsExpression(Expression) - Constructor for class net.sf.basedb.core.query.AbsExpression

ABSOLUTE - Enum constant in enum class net.sf.basedb.util.extensions.xml.PathType

Paths should be absolute paths from the root of the web server.

AbsoluteProgressReporter - Interface in net.sf.basedb.core

This is interface is an extension to the ProgressReporter interface.

ABSORBED_DOSE - Static variable in class net.sf.basedb.core.Quantity

The id for the Quantity object representing absorbed dose.

AbstractAnalysisPlugin - Class in net.sf.basedb.core.plugin

This is a base class that is useful for all analysis type plugins.

AbstractAnalysisPlugin() - Constructor for class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

Create a new AbstractAnalysisPlugin.

AbstractBatcher - Class in net.sf.basedb.core

This is an abstract class for batchers that are connected to a single DbControl object.

AbstractBatcher() - Constructor for class net.sf.basedb.core.AbstractBatcher

Constructor for a batcher.

AbstractBioAssaySetExporter - Class in net.sf.basedb.util.export.spotdata

An abstract superclass for all exporters that exports spot data from a bioassay set.

AbstractBioAssaySetExporter() - Constructor for class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

AbstractCustomRequestHandler - Class in net.sf.basedb.clients.jobagent.handlers

Abstract base class for custom request handler implementations.

AbstractCustomRequestHandler() - Constructor for class net.sf.basedb.clients.jobagent.handlers.AbstractCustomRequestHandler

AbstractDataWriterFactory<T> - Class in net.sf.basedb.util.bfs

Abstract implementation of a data writer factory.

AbstractDataWriterFactory(FilenameGenerator<T>) - Constructor for class net.sf.basedb.util.bfs.AbstractDataWriterFactory

Create a new factory that uses the given file name generator.

AbstractDbEngine - Class in net.sf.basedb.core.dbengine

An abstract superclass with default implementations for most DbEngine methods.

AbstractDbEngine() - Constructor for class net.sf.basedb.core.dbengine.AbstractDbEngine

Create AbstractDbEngine.

AbstractEntityQuery - Class in net.sf.basedb.core

An abstract implementation of the EntityQuery interface.

AbstractEntityQuery(Item, String, boolean) - Constructor for class net.sf.basedb.core.AbstractEntityQuery

Create a new query returning items of the specified item type using the default optional runtime filter.

AbstractEntityQuery(Item, String, boolean, QueryRuntimeFilter) - Constructor for class net.sf.basedb.core.AbstractEntityQuery

Create a new query returning items of the specified type with a non-default optional runtime filter.

AbstractEntityQuery(Item, Item, String, String, boolean, QueryRuntimeFilter) - Constructor for class net.sf.basedb.core.AbstractEntityQuery

Create a new query that may have different return type and root item type.

AbstractExporterPlugin - Class in net.sf.basedb.core.plugin

An abstract base class for all exporter plugins that wish to implement the ImmediateDownloadExporter interface.

AbstractExporterPlugin() - Constructor for class net.sf.basedb.core.plugin.AbstractExporterPlugin

Create a new AbstractExporterPlugin.

AbstractFieldConverter - Class in net.sf.basedb.util.export.spotdata

Abstract helper class for implementing ExportableFieldConverter.

AbstractFieldConverter(DbControl, BioAssaySet) - Constructor for class net.sf.basedb.util.export.spotdata.AbstractFieldConverter

Creates a new field converter to be used with a specific bioassay set source.

AbstractFilenameGenerator<T> - Class in net.sf.basedb.util.bfs

Abstract superclass for file names generator implementions that will help with ensuring that a generator creates unique file names.

AbstractFilenameGenerator() - Constructor for class net.sf.basedb.util.bfs.AbstractFilenameGenerator

AbstractFileUnpacker - Class in net.sf.basedb.util.zip

This is a base class for all plugins that wants to implement the FileUnpacker interface.

AbstractFileUnpacker() - Constructor for class net.sf.basedb.util.zip.AbstractFileUnpacker

AbstractFlatFileImporter - Class in net.sf.basedb.plugins

An abstract base class for all importers that imports data from one or more flat files.

AbstractFlatFileImporter() - Constructor for class net.sf.basedb.plugins.AbstractFlatFileImporter

AbstractHqlQuery - Class in net.sf.basedb.core

An abstract implementation of the HqlQuery interface.

AbstractHqlQuery(String, String, boolean) - Constructor for class net.sf.basedb.core.AbstractHqlQuery

Create a new HQL query.

AbstractIOSupport - Class in net.sf.basedb.plugins.executor

Abstract base class that is useful for plug-ins that need to implement the IOSupport interface and don't want to be visible as standalone plug-ins.

AbstractIOSupport() - Constructor for class net.sf.basedb.plugins.executor.AbstractIOSupport

AbstractItemImporter<I extends BasicItem> - Class in net.sf.basedb.plugins.batchimport

An abstract base class for plug-ins that import items in batch.

AbstractItemImporter() - Constructor for class net.sf.basedb.plugins.batchimport.AbstractItemImporter

AbstractJepConversionFunction<T> - Class in net.sf.basedb.util.jep.convert

Abstract superclass implementing the JepConversionFunction interface.

AbstractJepConversionFunction() - Constructor for class net.sf.basedb.util.jep.convert.AbstractJepConversionFunction

AbstractJspActionFactory<A extends Action> - Class in net.sf.basedb.clients.web.extensions

An abstract base class for action factories that may need to support adding scripts and stylesheets to the rendered JSP page.

AbstractJspActionFactory() - Constructor for class net.sf.basedb.clients.web.extensions.AbstractJspActionFactory

Create a new factory instance.

AbstractJspFactory - Class in net.sf.basedb.clients.web.extensions

An abstract BASE class for action and renderer factories.

AbstractJspFactory() - Constructor for class net.sf.basedb.clients.web.extensions.AbstractJspFactory

Create a new factory instance.

AbstractJspRendererFactory<A extends Action> - Class in net.sf.basedb.clients.web.extensions

An abstract base class for action factories that may need to support adding scripts and stylesheets to the rendered JSP page.

AbstractJspRendererFactory() - Constructor for class net.sf.basedb.clients.web.extensions.AbstractJspRendererFactory

Create a new factory instance.

AbstractListColumnBean<I,V> - Class in net.sf.basedb.clients.web.extensions.list

A simple bean-like implementation of the ListColumn interface.

AbstractListColumnBean() - Constructor for class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

AbstractNodeLoader<I> - Class in net.sf.basedb.util.overview.loader

Abstract node loader implementation that does nothing/throws an exception.

AbstractNodeLoader() - Constructor for class net.sf.basedb.util.overview.loader.AbstractNodeLoader

AbstractOnSaveAction - Class in net.sf.basedb.clients.web.extensions.edit

Abstract base implementation of the OnSaveAction interface.

AbstractOnSaveAction() - Constructor for class net.sf.basedb.clients.web.extensions.edit.AbstractOnSaveAction

Create a on-save action without a context

AbstractOnSaveAction(JspContext) - Constructor for class net.sf.basedb.clients.web.extensions.edit.AbstractOnSaveAction

Create a on-save action with a jsp context.

AbstractPlugin - Class in net.sf.basedb.core.plugin

This is an abstract base class useful for developing plugins.

AbstractPlugin() - Constructor for class net.sf.basedb.core.plugin.AbstractPlugin

Create a new AbstractPlugin.

AbstractQuery - Class in net.sf.basedb.core

An abstract implementation of the Query interface.

AbstractQuery(String) - Constructor for class net.sf.basedb.core.AbstractQuery

Create a new query.

AbstractQueryCache - Class in net.sf.basedb.core.hibernate

Abstract base class used to cache queries for a session.

AbstractQueryCache() - Constructor for class net.sf.basedb.core.hibernate.AbstractQueryCache

AbstractRenderer<A extends Action> - Class in net.sf.basedb.util.extensions

Abstract class that provides a default implementation of the deprecated AbstractRenderer.render(Action) method.

AbstractRenderer() - Constructor for class net.sf.basedb.util.extensions.AbstractRenderer

AbstractResultList<I> - Class in net.sf.basedb.core

This is a list of the result from a query.

AbstractResultList(long) - Constructor for class net.sf.basedb.core.AbstractResultList

AbstractResultWriter - Class in net.sf.basedb.core.migrate

Abstract base implementation of a result writer that simply store the result set, writer, etc. that are needed later.

AbstractResultWriter(ResultSet, int, Writer, char[]) - Constructor for class net.sf.basedb.core.migrate.AbstractResultWriter

Creates a new writer.

AbstractSignalHandler - Class in net.sf.basedb.core.signal

An abstract base class for signal handler implementations.

AbstractSignalHandler() - Constructor for class net.sf.basedb.core.signal.AbstractSignalHandler

Create a new signal handler, that initially doesn't support any signals at all.

AbstractSignalHandler(Collection<Signal>) - Constructor for class net.sf.basedb.core.signal.AbstractSignalHandler

Create a new signal handler that supports the given signals.

AbstractSignalReceiver - Class in net.sf.basedb.core.signal

Abstract base class that is useful when implementing signal receivers.

AbstractSignalReceiver() - Constructor for class net.sf.basedb.core.signal.AbstractSignalReceiver

Create a new signal receiver.

AbstractSignalTransporter - Class in net.sf.basedb.core.signal

Abstract base class that is useful when implementing signal transporters.

AbstractSignalTransporter() - Constructor for class net.sf.basedb.core.signal.AbstractSignalTransporter

AbstractSourceItemTransformer - Class in net.sf.basedb.util.listable

Abstract base class for source item transformers that can be useful for implementing some common functionality.

AbstractSourceItemTransformer(Item, Item) - Constructor for class net.sf.basedb.util.listable.AbstractSourceItemTransformer

Create a new instance that transforms between the given source and target item types.

AbstractSourceItemTransformerFactory - Class in net.sf.basedb.util.listable

Abstract base class for source item transformer factories that can be useful for implementing some common functionality.

AbstractSourceItemTransformerFactory(Item, Item[], Item[]) - Constructor for class net.sf.basedb.util.listable.AbstractSourceItemTransformerFactory

Create a new instance supports transformation between the given source items and target item.

AbstractSqlQuery - Class in net.sf.basedb.core

An abstract implementation of the SqlQuery interface.

AbstractSqlQuery(String) - Constructor for class net.sf.basedb.core.AbstractSqlQuery

AbstractSqlQuery.CountWork - Class in net.sf.basedb.core

ACCELERATION - Static variable in class net.sf.basedb.core.Quantity

The id for the Quantity object representing acceleration.

accept(File) - Method in class net.sf.basedb.util.OlderThanFileFilter

Accept files that are older than the specified last modified time.

accept(File) - Method in class net.sf.basedb.util.RegexpFileFilter

Accept files with a name matching the regular expression

accept(String) - Method in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget

Accept - Enum Class in net.sf.basedb.util.fileset

Return result from the ValidationAction.acceptFile(net.sf.basedb.core.FileSetMember) method.

Accept() - Constructor for enum class net.sf.basedb.util.fileset.Accept

acceptDenied - Variable in class net.sf.basedb.util.overview.validator.NullNodeValidator

acceptedFile - Variable in class net.sf.basedb.util.fileset.SingleFileValidationAction

acceptFile(FileSetMember) - Method in class net.sf.basedb.util.fileset.SingleFileValidationAction

If the file has a file type matching the id given in the constructor it is accepted for immediate validation.

acceptFile(FileSetMember) - Method in interface net.sf.basedb.util.fileset.ValidationAction

Check if the given file is handled by this validator implementation or not?

acceptInsertIfNullReporterOnFeature - Variable in class net.sf.basedb.core.RawDataBatcher

If we should always accept inserts when the feature has a NULL reporter.

acceptInsertIfNullReporterOnFeature(boolean) - Method in class net.sf.basedb.core.RawDataBatcher

Specify if inserts always should be accepted if there is a matching feature that has a NULL reporter.

acceptMissing - Variable in class net.sf.basedb.util.overview.validator.NullNodeValidator

AccessControlled - Interface in net.sf.basedb.core

This interface should be implemented by a class representing items which requires the logged in user to have permission to access them.

AccountExpiredException - Exception in net.sf.basedb.core

This exception is thrown if you try to log in with an account that has expired.

AccountExpiredException(String, Date) - Constructor for exception net.sf.basedb.core.AccountExpiredException

Creates a new AccountExpiredException.

aColumn - Static variable in class net.sf.basedb.util.importer.spotdata.MAParser

ACT_AS_ANOTHER_USER - Enum constant in enum class net.sf.basedb.core.Permission

This permission allows a user act as another user using the SessionControl.impersonateLogin(int, String) method.

action - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemExtensionColumn

action - Variable in class net.sf.basedb.clients.web.taglib.table.Table

Action - Interface in net.sf.basedb.util.extensions

An action is an object that is added to an ExtensionPoint by an Extension.

Action() - Constructor for enum class net.sf.basedb.core.Transactional.Action

actionClass - Variable in class net.sf.basedb.util.extensions.ExtensionPointBean

actionClass - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint

ActionClassEventFilter - Class in net.sf.basedb.util.extensions.events

Event filter that only passes on events to extension points with a given action class.

ActionClassEventFilter(Class<? extends Action>) - Constructor for class net.sf.basedb.util.extensions.events.ActionClassEventFilter

Create a new action class filter.

actionFactory - Variable in class net.sf.basedb.util.extensions.ExtensionBean

actionFactory - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtension

ActionFactory<A extends Action> - Interface in net.sf.basedb.util.extensions

An action factory is an object which knows how to create Action:s.

actionId - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

ActionIterator<A extends Action> - Class in net.sf.basedb.util.extensions

Iterator for iterating over all actions that will be created by extensions after a call to Registry.useExtensions(ClientContext, ExtensionsFilter, String...).

ActionIterator(Iterator<ExtensionContext<A>>) - Constructor for class net.sf.basedb.util.extensions.ActionIterator

actions - Variable in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

actions - Variable in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory

actions - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory

actions - Variable in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory

actions - Variable in class net.sf.basedb.util.extensions.ActionIterator

actions - Variable in class net.sf.basedb.util.extensions.debug.BeanActionFactory

actions - Variable in class net.sf.basedb.util.extensions.debug.ProxyActionFactory

active - Variable in class net.sf.basedb.clients.web.taglib.tab.TabControl

The ID attribute of the active tab.

activeJobs - Variable in class net.sf.basedb.clients.jobagent.Agent

activeProject - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

activeProject - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

activeProjectId - Variable in class net.sf.basedb.core.AnnotationBatcher

activeProjectId - Variable in class net.sf.basedb.core.data.JobData

activeProjectId - Variable in class net.sf.basedb.core.SessionControl.LoginInfo

The id of the ProjectData object of the active project.

activeProjectName - Variable in class net.sf.basedb.core.SessionControl.LoginInfo

The name of the the active project.

actualCatalog - Variable in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration

actualParameters - Variable in class net.sf.basedb.util.jep.SimpleJepFunction

actualSchema - Variable in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration

AdaptiveNumberFormatter - Class in net.sf.basedb.util.formatter

Formats a number for output on a web page adapting thwe number of decimals depending on the order of magnitude of the value.

AdaptiveNumberFormatter(int, boolean) - Constructor for class net.sf.basedb.util.formatter.AdaptiveNumberFormatter

Create a new number formatter.

add(int, I) - Method in class net.sf.basedb.core.AbstractResultList

Not supported.

add(int, T) - Method in class net.sf.basedb.core.UnmodifiableResultList

Not supported.

add(E) - Method in class net.sf.basedb.util.Tree

Not supported.

add(I) - Method in class net.sf.basedb.core.AbstractResultList

Not supported.

add(Long, Long) - Method in class net.sf.basedb.core.DiskUsageStatistics.Summary

add(Collection<? extends Integer>) - Method in class net.sf.basedb.core.ItemList

Add all items in the collection to this list.

add(Iterator<? extends Listable>) - Method in class net.sf.basedb.core.ItemList

Add multiple items to this list in one go.

add(K, V) - Method in class net.sf.basedb.util.Enumeration

add(DerivedBioAssayData) - Method in class net.sf.basedb.core.DerivedBioAssay.FixDerivedBioAssayParentsRecursivelyAction

Register the given derived bioassay as one that has had it's parent items changed.

add(SystemData) - Static method in class net.sf.basedb.core.SystemItems

Register a system item.

add(ItemQuery<? extends Listable>) - Method in class net.sf.basedb.core.ItemList

Add all items that are returned by the query to this list.

add(Listable) - Method in class net.sf.basedb.core.ItemList

Add an item to this list.

add(Listable) - Method in class net.sf.basedb.core.ItemList.DelayedAdditionManager

add(Expression, Expression) - Static method in class net.sf.basedb.core.query.Expressions

Add two expressions: new expression = e1 + e2.

add(InheritSpecification) - Method in class net.sf.basedb.util.annotations.InheritAnnotationsManager.AnnotationTypeFilter

add(LogEntry) - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog

Add a log entry.

add(T) - Method in class net.sf.basedb.core.ItemResultList.ResultListListIterator

This operation is not supported.

add(T) - Method in class net.sf.basedb.core.UnmodifiableResultList

Not supported.

ADD - Enum constant in enum class net.sf.basedb.core.log.ChangeType

ADD_MEMBERS - Static variable in class net.sf.basedb.clients.web.ModeInfo

Mode for adding members to an item list.

ADD_ONLY - Enum constant in enum class net.sf.basedb.core.ItemList.SynchronizeOption

Synchronize the members by adding new items matching the filter.

addAll(int, Collection<? extends I>) - Method in class net.sf.basedb.core.AbstractResultList

Not supported.

addAll(int, Collection<? extends T>) - Method in class net.sf.basedb.core.UnmodifiableResultList

Not supported.

addAll(Collection<? extends E>) - Method in class net.sf.basedb.util.Tree

Not supported.

addAll(Collection<? extends I>) - Method in class net.sf.basedb.core.AbstractResultList

Not supported.

addAll(Collection<? extends T>) - Method in class net.sf.basedb.core.UnmodifiableResultList

Not supported.

addAll(ItemList) - Method in class net.sf.basedb.core.ItemList

Add all items from another item list to this list.

addAll(ItemList.DelayedAdditionManager) - Method in class net.sf.basedb.core.ItemList.DelayedAdditionManager

addAll(ReporterList) - Method in class net.sf.basedb.core.ReporterList

Add all reporters from another reporter list to this list.

addAllItems(Collection<? extends Annotatable>) - Method in class net.sf.basedb.util.annotations.RunnableInheritAnnotationsManager

Add all items for processing.

AddAllTransformer<I> - Class in net.sf.basedb.util.collections

Collection transformer implementation that adds all elements in the source collection to the destination collection.

AddAllTransformer() - Constructor for class net.sf.basedb.util.collections.AddAllTransformer

addAnnotatableParents(DbControl, Set<Annotatable>, AnnotatableData...) - Method in class net.sf.basedb.core.BasicItem

Try to load the the item-class representation of all the data-class items ignoring permission problems.

addAnnotationTypes(Collection<AnnotationType>) - Method in class net.sf.basedb.core.AnnotationBatcher

Add annotation types to work with.

addArrayDesignBlock(BlockInfo) - Method in class net.sf.basedb.core.ArrayDesign

Adds an ArrayDesignBlock to the array design.

addAssayField(AssayField) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

Add information about an assay field that should be exported.

addAssayField(AssayField) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter

Adds an assay field to the exported file.

addAssayField(AssayField) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter

addAssayFields(Collection<? extends AssayField>) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter

Add multiple assay fields in one go.

addAssayFields(Collection<? extends AssayField>) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter

Add multiple assay fields in one go.

addAttributes(StringBuilder, Iterator<DynamicActionAttribute>) - Static method in class net.sf.basedb.clients.web.extensions.DynamicActionAttributeSupport

Append all dynamic action attributes to the string builder.

addAutoJoiner(AutoJoiner<?, ?>) - Method in class net.sf.basedb.core.AbstractQuery

addAutoJoiner(AutoJoiner<?, ?>) - Method in interface net.sf.basedb.core.query.Query

addBatcher(Batcher) - Method in class net.sf.basedb.core.DbControl

Add a Batcher to the batcher queue.

addButton(String) - Method in class net.sf.basedb.clients.web.taglib.ButtonGroup

addBytes(long) - Method in class net.sf.basedb.core.DataCube

addBytes(long) - Method in class net.sf.basedb.core.DataCubeExtraValue

addBytes(long) - Method in class net.sf.basedb.core.DataCubeFilter

addBytes(long) - Method in class net.sf.basedb.core.DataCubeLayer

addBytes(long) - Method in class net.sf.basedb.core.Experiment

addBytes(long) - Method in class net.sf.basedb.core.ReporterCloneTemplate

addCategory(AnnotationTypeCategory) - Method in class net.sf.basedb.core.AnnotationType

Add a category to this annotation type.

addChange(ChangeType, Object, Object[], Object[], String[], Type[], boolean) - Method in class net.sf.basedb.core.log.LoggingInterceptor

If the log manager factory creates an entity logger, add information about the change to the internal list.

addCheckedSource(BioMaterial) - Method in class net.sf.basedb.core.BioMaterialEvent

addChild(E) - Method in class net.sf.basedb.util.Tree.Entry

Add a child to the node.

addChild(Node) - Method in class net.sf.basedb.util.overview.Node

Add a child node to this one.

addChildAssay(BaseFileInfo.ChildBioAssay) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo

Add information about a child assay.

addChildBioAssaySets(BioAssaySetData, Set<BioAssaySetData>) - Method in class net.sf.basedb.core.BioAssaySet

Find all bioassaysets that are children to the specified parent (ie.

addChildElements(Map<QueryElement, Object>, QueryElement) - Method in class net.sf.basedb.core.AbstractQuery

addChildEntry(Tree.Entry<E>) - Method in class net.sf.basedb.util.Tree.Entry

addChildErrors(int) - Method in class net.sf.basedb.util.overview.Node

Add child errors to this node.

addChildReporter(Integer, Integer) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo

Add a child position/reporter mapping from the parsed BASEfile.

addChildWarnings(int) - Method in class net.sf.basedb.util.overview.Node

Add child warnings to this node.

addClonableProperty(ClonableProperty) - Method in class net.sf.basedb.core.ReporterCloneTemplate

Add a clonable property to this template.

addColumn(MetadataImplementor, Table, VirtualColumn) - Static method in class net.sf.basedb.core.HibernateUtil

Add a column to a table.

addColumnDef(ColumnDef, ListColumnAction) - Method in class net.sf.basedb.clients.web.taglib.table.Table

AddConverter - Class in net.sf.basedb.util.jep.convert

Convert Add function to a Query API Expression.

AddConverter() - Constructor for class net.sf.basedb.util.jep.convert.AddConverter

addData(SqlResultIterator, String...) - Method in class net.sf.basedb.util.plot.ScatterPlot

Add data to the plot.

addData(SqlResultIterator, String, float, HistogramPlot.YAggregate, HistogramPlot.YAggregate) - Method in class net.sf.basedb.util.plot.HistogramPlot

Add data to the plot.

addData(SqlResultIterator, Collection<PlotAnnotation>) - Method in class net.sf.basedb.util.plot.ScatterPlot

Add data to the plot.

addData(SqlResultIterator, Collection<PlotAnnotation>, float, HistogramPlot.YAggregate, HistogramPlot.YAggregate) - Method in class net.sf.basedb.util.plot.HistogramPlot

Add data to the plot.

addDataParser(DataParser) - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser

Adds a data parser.

addDefaultItem(BasicItem) - Method in class net.sf.basedb.core.Project

Add an item as a default project item.

addDefultRolesAndGroups(Session, UserData) - Static method in class net.sf.basedb.core.User

Add all groups and roles that has been marked as default to the user.

addDirectory(File) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager

Add a directory to this manager.

addDynamicAttributes(StringBuilder) - Method in class net.sf.basedb.clients.web.taglib.StylableTag

ADDED - Enum constant in enum class net.sf.basedb.core.AnnotationBatcher.Change

A new annotation was created.

addedBytes - Variable in class net.sf.basedb.core.DataCube

addedBytes - Variable in class net.sf.basedb.core.Experiment

addEntity(Class) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

addEntity(String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

addEntity(String, Class) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

addEntity(String, Class, LockMode) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

addEntity(String, String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

addEntity(String, String, LockMode) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

addEntry(String, String...) - Method in class net.sf.basedb.util.bfs.MetadataModel.Section

Add a new entry to this section.

addEntry(MetadataModel.SectionEntry) - Method in class net.sf.basedb.util.bfs.MetadataModel.Section

Add a new entry to this section.

addEntry(Tree.Entry<E>) - Method in class net.sf.basedb.util.Tree

addError(String) - Method in class net.sf.basedb.util.jep.FunctionSafeJep

Adds an error message to the "real" JEP parser.

addErrorHandler(Class<? extends Throwable>, ErrorHandler) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

Add an error handler for the specified class of error.

addErrorHandler(Class<? extends Throwable>, ErrorHandler) - Method in class net.sf.basedb.util.error.ClassMapErrorHandler

Add an error handler for throwable:s of a specific class.

addErrorMessage(ExtensionsFile, String) - Method in class net.sf.basedb.util.extensions.manager.ProcessResults

Adds a detailed message inidcating a failed operation to a file.

addErrors(int) - Method in class net.sf.basedb.util.overview.Node

Add more errors to this node.

addEventHandler(EventHandler) - Method in class net.sf.basedb.util.bfs.MultiEventHandler

Adds an event handler.

addEventListeners(SessionEventListener...) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

addExperimentalFactor(AnnotationType) - Method in class net.sf.basedb.core.Experiment

Add an annotation type as an experimental factor to this experiment.

addExperimentalFactorsAsAssayFields() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

Adds all experimental factors from the experiment that the source bioassay set belongs to as assay fields.

addExperimentParameters(DbControl, Experiment, List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter

AddExpression - Class in net.sf.basedb.core.query

Add two expressions: e1 + e2.

AddExpression(Expression, Expression) - Constructor for class net.sf.basedb.core.query.AddExpression

addExtendedProperties(Element, String) - Static method in class net.sf.basedb.core.HibernateUtil

Append <property> tags to the given class tag.

addExtension(Registry.RegisteredExtension<A>) - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint

Add an extension to this extension point.

addExtensionsFile(ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager

addExtraColumns(List<TableColumn>, DbControl, BioAssaySet, String, String, String) - Static method in class net.sf.basedb.clients.web.DynamicUtil

addExtraFile(String, String) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter

Add information about an extra data file that is included as part of the BFS.

addExtraFloat(DbControl, String) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo

Add information about an extra float value that appears in the BASEfile.

addExtraFloatParser(ExtraFloatParser) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo

Add an extra value parser to this section.

addFetch(String, String, String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

addFile(File) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager

Add a file to the manager that is supposed to contain extensions.

addFile(String, String) - Method in class net.sf.basedb.util.bfs.MetadataModel

Add an entry to the 'files' section.

addFile(String, UploadedFile) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload

Store information about an uploaded file.

addFilename(String) - Method in class net.sf.basedb.util.bfs.AbstractFilenameGenerator

Add the file name to the list of already generated file names.

addFilter - Variable in class net.sf.basedb.clients.web.SubContext

AddFilter() - Constructor for enum class net.sf.basedb.core.ItemContext.AddFilter

addFilterConditions(Element, String, HibernateUtil.FilterConfigurator) - Static method in class net.sf.basedb.core.HibernateUtil

Add <filter> conditions to the given class tag.

addFilteredColumn(String, String, boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Table

addFilterRows(int) - Method in class net.sf.basedb.core.ItemContext

Add filter rows to the table.

addFix(Fix) - Method in class net.sf.basedb.util.overview.Failure

Add a suggested fix to this failure.

addFormulaColumns(List<TableColumn>, DbControl, RawDataType, Formula.Type, IntensityTransform, String, String, boolean) - Static method in class net.sf.basedb.clients.web.DynamicUtil

addFunctions(JEP, JepFunction...) - Static method in class net.sf.basedb.util.jep.Jep

addGroup(Group) - Method in class net.sf.basedb.core.Group

Add a group as a member to this group.

addHeaderColumns(int) - Method in class net.sf.basedb.clients.web.taglib.table.HeaderRow

addHidden(String, String) - Method in class net.sf.basedb.clients.web.taglib.table.Table

addIdAndStyles(StringBuilder, String...) - Method in class net.sf.basedb.clients.web.taglib.StylableTag

Add id, class and style attributes the the stringbuilder.

addIfPresentIn(int, int, Collection<ItemList>) - Method in class net.sf.basedb.core.ItemList

Add items that are present in the specified number of lists to this list.

addIfPresentIn(int, int, Collection<ReporterList>) - Method in class net.sf.basedb.core.ReporterList

Add reporters that are present in the specified number of lists to this list.

addIgnore(File) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager

Add a file to the ignore list.

addIntersection(Collection<ItemList>) - Method in class net.sf.basedb.core.ItemList

Add items that are present in ALL OF the given lists to this list.

addIntersection(Collection<ReporterList>) - Method in class net.sf.basedb.core.ReporterList

Add reporters that are present in ALL OF the given lists to this list.

addItem(Annotatable) - Method in class net.sf.basedb.util.annotations.RunnableInheritAnnotationsManager

Add an item that should inherit annotations.

addJoin(String, String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

addJoin(String, String, String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

addJoin(String, String, LockMode) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

addManualSingleChange(ChangeType, Object) - Method in class net.sf.basedb.core.log.LoggingInterceptor

Adds a manual non-Hibernate change to the log system.

addManualSingleChange(ChangeType, Object, Object, Object, String, Type) - Method in class net.sf.basedb.core.log.LoggingInterceptor

Adds a manual non-Hibernate change to the log system.

addMeasurement(float) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin

Add a measurement to this bin.

addMember(File, DataFileType) - Method in class net.sf.basedb.core.FileSet

Add a file as a member to the file set.

addMembers(Set<Integer>, ItemList.DelayedAdditionManager) - Method in class net.sf.basedb.core.ItemList

Add members to this list.

addMembersMode - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

addMenuitem(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Menu

addMessage(ExtensionsFile, String) - Method in class net.sf.basedb.util.extensions.manager.ProcessResults

Adds a detailed message indicating a successful operation to a file.

addMessage(ExtensionsFile, String, boolean) - Method in class net.sf.basedb.util.extensions.manager.ProcessResults

addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Add column mapping parameters for item-specific properties.

addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

Adds column mappings for name and description.

addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter

Adds column mappings for name, description, protocol, robot, and array design

addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter

Adds column mappings for name, externalId, description, protocol, creation date, original quantity, pooled, parent and used quantity from parent.

addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.ArraySlideImporter

Adds column mappings for name, description, array batch, batch index, barcode and destroyed

addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.BioPlateImporter

Adds column mappings for name, description, plate type, plate geometry, barcode and freezer.

addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.BioSourceImporter

Adds column mappings for name, externalId and description.

addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

Adds column mappings for name, internalId, subtype, description, protocol, hardware, software, parent, data files and permissions.

addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.ExtractImporter

Adds column mappings for name, externalId, description, protocol, creation date, original quantity, pooled, parent and used quantity from parent.

addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.FileImporter

Adds column mappings for name, externalId and description.

addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.KitImporter

Adds column mappings for name and description.

addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter

Adds column mappings for name, externalId, description, protocol, creation date, original quantity, pooled, parent and used quantity from parent.

addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

Adds column mappings for name, externalId, description, protocol, creation date, original quantity, pooled, parent and used quantity from parent.

addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.SampleImporter

Adds column mappings for name, externalId, description, protocol, creation date, original quantity, pooled, parent and used quantity from parent.

addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.TagImporter

Adds column mappings for name and description.

addMoreErrorParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Add extra parameters to the "Error handling" section that the subclass needs.

addMoreErrorParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter

addMoreJobParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Add extra job parameters that the subclass needs.

addMoreJobParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter

Add parameter for "Data directory" directory where data files may be located.

addMoreJobParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

Add parameter for "Data directory" directory where data files may be located.

addMoreJobParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.FileImporter

addMoreJobParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

Add parameter for "Data directory" directory where data files may be located.

addMoreParsingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Add extra parameters to the "Parser settings" section that the subclass needs.

addMoreParsingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

addParameter(String, String) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload

Store the value of a regular form field.

addParameter(AnnotationType) - Method in class net.sf.basedb.core.Protocol

Add an annotation type as a parameter to this protocol.

addParametersWithNamespace(List<PluginParameter<?>>, List<PluginParameter<?>>, String) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

Add more parameters to a list of parameters with a different namespace.

addParent(DerivedBioAssay) - Method in class net.sf.basedb.core.DerivedBioAssay

Add a derived bioassay as a parent to this derived bioassay.

addParticipant(BioPlate, String, int) - Method in class net.sf.basedb.core.BioPlateEvent

Add a bioplate as a participant in this event.

addPermissions(Group, Set<Permission>) - Method in class net.sf.basedb.core.GroupPermissions

Grant permissions to a group, keeping those that have already been set.

addPermissions(Group, Set<Permission>) - Method in class net.sf.basedb.core.MultiPermissions

Grant permissions to a group, keeping those that have already been set.

addPermissions(Project, Set<Permission>) - Method in class net.sf.basedb.core.MultiPermissions

Grant permissions to a project, keeping those that have already been set.

addPermissions(Project, Set<Permission>) - Method in class net.sf.basedb.core.ProjectPermissions

Grant permissions to a project, keeping those that have already been set.

addPermissions(User, Set<Permission>) - Method in class net.sf.basedb.core.MultiPermissions

Grant permissions to a user, keeping those that have already been set.

addPermissions(User, Set<Permission>) - Method in class net.sf.basedb.core.UserPermissions

Grant permissions to a user, keeping those that have already been set.

addPhysicalBioAssay(PhysicalBioAssay) - Method in class net.sf.basedb.core.DerivedBioAssay

Add a physical bioassay as a parent to this derived bioassay.

addPlate(Plate) - Method in class net.sf.basedb.core.ArrayDesign

Adds a single plate to the plate list.

addQueryHint(String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

addQueryHint(String) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

addRawBioAssay(RawBioAssay) - Method in class net.sf.basedb.core.Experiment

Add a raw bioassay to this experiment.

addRawBioAssayParameters(DbControl, RawBioAssay, List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter

addRawDataColumns(List<TableColumn>, DbControl, RawDataType, String, String, String) - Static method in class net.sf.basedb.clients.web.DynamicUtil

addRawDataMappings(MetadataSources) - Static method in class net.sf.basedb.core.HibernateUtil

Generate additional mappings for the raw data types.

addReplaceSection - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

addReporter(ReporterData, Float) - Method in class net.sf.basedb.core.ReporterList

Add or update the score for a reporter.

addReporterColumns(List<TableColumn>, DbControl, String, String, String) - Static method in class net.sf.basedb.clients.web.DynamicUtil

addReporterColumns(List<TableColumn>, DbControl, ReporterCloneTemplate, String, String, String) - Static method in class net.sf.basedb.clients.web.DynamicUtil

addReporterField(DynamicField) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

Add information about a reporter field that should be exported.

addReporterField(DynamicField) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter

addReporterField(DynamicField) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter

addReporterFields(Collection<? extends DynamicField>) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter

Add multiple reporter fields in one go.

addReporterFields(Collection<? extends DynamicField>) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter

Add multiple reporter fields in one go.

addReporters(Set<Integer>) - Method in class net.sf.basedb.core.ReporterList

addReportUriIfNeeded(String, FilterConfig) - Method in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter

addResources(Vector<URL>, Enumeration<URL>) - Method in class net.sf.basedb.util.JarClassLoader

address - Variable in class net.sf.basedb.core.authentication.ExtraUserInformation

address - Variable in class net.sf.basedb.core.data.UserData

addRestriction(Restriction) - Method in class net.sf.basedb.core.ItemContext.RowRestrictions

addRoleKey(RoleKeyData) - Static method in class net.sf.basedb.core.SystemItems

Register a role key.

addRolePermissions(RoleData, Map<Item, Integer>) - Static method in class net.sf.basedb.core.Install

Add permissions for a role for specific item types.

addRoot(String, Class) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

addRoot(String, String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

addRow(String...) - Method in class net.sf.basedb.util.bfs.AnnotationModel

Add a row of data to the model.

addRow(String...) - Method in class net.sf.basedb.util.bfs.MatrixModel

Add a row of data to the model.

addScalar(String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

addScalar(String, Type) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

addScript(String) - Method in class net.sf.basedb.clients.web.extensions.JspContext

Add an absolute reference to a script that should be included on the generated page with a <script> tag.

addScripts(Collection<String>) - Method in class net.sf.basedb.clients.web.extensions.JspContext

Add several scripts in one go.

addSection(String) - Method in class net.sf.basedb.util.bfs.MetadataModel

Adds a new section to the model.

addSeries(HistogramPlot.HistogramSeries) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset

addSignal(Signal) - Method in class net.sf.basedb.core.signal.AbstractSignalHandler

Add a signal to the list of supported signals.

addSource(BioMaterial) - Method in class net.sf.basedb.core.BioMaterialEvent

Add a biomaterial as a source to this event.

addSpecification(InheritSpecification) - Method in class net.sf.basedb.util.annotations.RunnableInheritAnnotationsManager

Add a specification with rules for inheriting annotations.

addSpotColumns(List<TableColumn>, DbControl, int, IntensityTransform) - Static method in class net.sf.basedb.clients.web.DynamicUtil

addSpotField(DynamicField) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

Add information about a spot field that should be exported.

addSpotField(DynamicField) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter

addSpotField(DynamicField) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter

Add information about a spot field that should be exported.

addSpotFields(Collection<? extends DynamicField>) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter

Add multiple spot fields in one go.

addSpotFields(Collection<? extends DynamicField>) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter

Add multiple spot fields in one go.

addSpotIntensityParser(SpotIntensityParser) - Method in class net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser

Adds a spot intensity parser to the list of used parsers.

addSpotSectionInfo(int, BaseFileInfo.SpotSectionInfo) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo

Adds information about a 'spot' section.

addSqlFunctions(SessionFactoryBuilder, DbEngine) - Static method in class net.sf.basedb.core.HibernateUtil

Add more SQL functions to HQL that are not present in a standard Hibernate installation.

addStaticMappings(MetadataSources, HibernateUtil.FilterConfigurator) - Static method in class net.sf.basedb.core.HibernateUtil

Read all mapping files, which must be named Class.hbm.xml where class is the name of each class.

addStatistics(String, float) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup

Add another statisitcal measurement to this group.

addStylesheet(String) - Method in class net.sf.basedb.clients.web.extensions.JspContext

Add an absolute reference to a CSS stylesheet that should be included on the generated page with a <link> tag.

addStylesheets(Collection<String>) - Method in class net.sf.basedb.clients.web.extensions.JspContext

Add several stylesheets in one go.

addSymbol(String) - Method in class net.sf.basedb.core.Unit

Add a symbol to this unit.

addSynchronizedEntityClass(Class) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

addSynchronizedEntityName(String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

addSynchronizedQuerySpace(String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

addTab(TabAction) - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl

addToBatch(D, PreparedStatement, List<BatchedPropertyInfo>) - Method in class net.sf.basedb.core.BasicBatcher

Add the data object to the batch represented by the prepared statement

addToBatch(Object...) - Method in class net.sf.basedb.core.AnnotationBatcher.UpdateBatcher

Add a new entry to the batch.

addToDefaultRolesAndGroups() - Method in class net.sf.basedb.core.User

Add this user to the groups and roles that has been marked as default for new users.

addToUnlimited - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

addToUnlimitedParameter - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

addTransactionalAction(TransactionalAction) - Method in class net.sf.basedb.core.DbControl

Add a transactional action to this DbControl.

addTransferredBytes(long) - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress

Adds a value to the number of transfered bytes.

addUnion(Collection<ItemList>) - Method in class net.sf.basedb.core.ItemList

Add items that are present in at least ONE OF the given lists to this list.

addUnion(Collection<ReporterList>) - Method in class net.sf.basedb.core.ReporterList

Add reporters that are present in at least ONE OF the given lists to this list.

addURI(URI) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager

Add an URI that points to an XML file containing definitions.

addUsableUnit(Unit) - Method in class net.sf.basedb.core.AnnotationType

Add a unit to be used with this annotation type.

addUsedQuantity(float) - Method in class net.sf.basedb.core.MeasuredBioMaterial.RemainingQuantityAction

Add some used quantity to what has currently been recorded.

addUser(User) - Method in class net.sf.basedb.core.Group

Add a user as a member to this group.

addUser(User) - Method in class net.sf.basedb.core.Role

Assign this Role to a user.

addUsingItems(Set<ItemProxy>, Item, Query<Integer>) - Method in class net.sf.basedb.core.BasicItem

Add items to the set of items using this one.

addUsingItems(Set<ItemProxy>, Query<? extends BasicData>) - Method in class net.sf.basedb.core.BasicItem

Add items to the set of items using this one.

addValue(int, float) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup

Add an intensity value to this group.

addValue(AnnotationType, Object, Unit, boolean) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations

Add an annotation value.

addValueConverter(ValueConverter) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader

Add a value converter to this loader

addWarnings(int) - Method in class net.sf.basedb.util.overview.Node

Add more warnings to this node.

adjustExistingItems(ProgressReporter, int, String, String) - Static method in class net.sf.basedb.core.Update

Adjust the existing items in the database to be compatible with the latest mappings.

adjustRanges() - Method in class net.sf.basedb.util.plot.HistogramPlot

Auto-size of the x and y range doesn't seem to work, so we have to do it manually.

ADMINISTRATOR - Static variable in class net.sf.basedb.core.Role

The id for the Role item representing adminstrators.

AdvancedFieldConverter - Class in net.sf.basedb.util.export.spotdata

Field converter implementation that gives more detailed control how fields are converted and used in the export.

AdvancedFieldConverter(DbControl, BioAssaySet) - Constructor for class net.sf.basedb.util.export.spotdata.AdvancedFieldConverter

Create a new advanced field converter.

affiliations - Variable in class net.sf.basedb.core.data.ExperimentData

AFFYMETRIX - Static variable in class net.sf.basedb.core.Platform

The external id for the Affymetrix platform.

AFFYMETRIX_CDF - Static variable in class net.sf.basedb.core.DataFileType

The external ID for the file type representing Affymetrix CDF files.

AFFYMETRIX_CEL - Static variable in class net.sf.basedb.core.DataFileType

The external ID for the file type representing Affymetrix CEL files.

AffymetrixUtil - Class in net.sf.basedb.util.affymetrix

Utility class with Affymetrix-related functionality.

AffymetrixUtil() - Constructor for class net.sf.basedb.util.affymetrix.AffymetrixUtil

aFloat(float) - Static method in class net.sf.basedb.core.query.Expressions

Create a constant expression from a float.

AFTER_ENABLE - Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl

This event is sent after an extension or extension point is enabled by ExtensionsControl.enableExtensionPoint(String, boolean), ExtensionsControl.enableExtension(String, boolean), or ExtensionsControl.enableAllInFile(String, boolean).

AFTER_REGISTRATION - Static variable in class net.sf.basedb.util.extensions.events.EventType

This event is sent after an extension or extension point has been registered with a registry.

AFTER_UPDATE - Static variable in class net.sf.basedb.util.extensions.events.EventType

This event is sent during an update of an existing extension point or extension.

afterCommit() - Method in class net.sf.basedb.core.log.db.DbLogManager

afterCommit() - Method in interface net.sf.basedb.core.log.LogManager

Called after a successful commit of changes to the database.

afterRollback() - Method in class net.sf.basedb.core.log.db.DbLogManager

afterRollback() - Method in interface net.sf.basedb.core.log.LogManager

Called after rollback.

afterTransactionCompletion(Transaction) - Method in class net.sf.basedb.core.log.LoggingInterceptor

Signals successful commit or rollback to the log manager.

agent - Variable in class net.sf.basedb.clients.jobagent.AgentSignalReceiver

agent - Variable in class net.sf.basedb.clients.jobagent.handlers.AbstractCustomRequestHandler

agent - Variable in class net.sf.basedb.clients.jobagent.handlers.DefaultRequestHandler

agent - Variable in class net.sf.basedb.clients.jobagent.handlers.InfoRequestHandler

agent - Variable in class net.sf.basedb.clients.jobagent.handlers.MultiProtocolRequestHandler

agent - Variable in class net.sf.basedb.clients.jobagent.handlers.PauseRequestHandler

agent - Variable in class net.sf.basedb.clients.jobagent.handlers.SignalRequestHandler

agent - Variable in class net.sf.basedb.clients.jobagent.handlers.StartRequestHandler

agent - Variable in class net.sf.basedb.clients.jobagent.handlers.StopRequestHandler

agent - Variable in class net.sf.basedb.clients.jobagent.JobQueueChecker

agent - Variable in class net.sf.basedb.clients.jobagent.JobRunner

agent - Variable in class net.sf.basedb.clients.jobagent.slotmanager.InternalSlotManager

agent - Variable in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager

agent - Variable in class net.sf.basedb.core.Job.ProgressReporterImpl

Agent - Class in net.sf.basedb.clients.jobagent

This is the actual job agent application.

Agent(Properties) - Constructor for class net.sf.basedb.clients.jobagent.Agent

Create a new job agent.

AgentController - Class in net.sf.basedb.clients.jobagent

This is the command line controller class for the job agent application.

AgentController(Properties) - Constructor for class net.sf.basedb.clients.jobagent.AgentController

Create a new controller for controlling the job agent specified by the given properties.

agentInfo - Static variable in class net.sf.basedb.core.JobAgent

AgentSignalReceiver - Class in net.sf.basedb.clients.jobagent

Signal receiver implementation for job agents that is compatible with the SocketSignalReceiver.

AgentSignalReceiver(Agent) - Constructor for class net.sf.basedb.clients.jobagent.AgentSignalReceiver

agentVersionForJobQuery - Variable in class net.sf.basedb.clients.jobagent.JobQueueChecker

The job agent's version when the query was cached.

Aggregations - Class in net.sf.basedb.core.query

A factory class to create aggregate expressions.

Aggregations() - Constructor for class net.sf.basedb.core.query.Aggregations

aIndex - Variable in class net.sf.basedb.util.importer.spotdata.MAParser

alias - Variable in class net.sf.basedb.core.AnnotationRestriction

alias - Variable in enum class net.sf.basedb.core.Item

alias - Variable in class net.sf.basedb.core.query.AnnotationExpression

alias - Variable in class net.sf.basedb.core.query.AnnotationJoin

alias - Variable in class net.sf.basedb.core.query.AnyToAnyRestriction

alias - Variable in class net.sf.basedb.core.query.ExpressionSelect

alias - Variable in class net.sf.basedb.core.query.HqlElementsExpression

alias - Variable in class net.sf.basedb.core.query.HqlIndexExpression

alias - Variable in class net.sf.basedb.core.query.HqlInnerJoin

alias - Variable in class net.sf.basedb.core.query.HqlLeftJoin

alias - Variable in class net.sf.basedb.core.query.HqlPropertyExpression

alias - Variable in class net.sf.basedb.core.query.HqlRightJoin

alias - Variable in class net.sf.basedb.core.query.HqlSizeExpression

alias - Variable in class net.sf.basedb.core.query.SqlColumnExpression

alias - Variable in class net.sf.basedb.core.RealTable

The alias to use in queries for this table.

alias - Variable in enum class net.sf.basedb.core.VirtualTable

The alias to use in queries for this table.

alias - Variable in class net.sf.basedb.util.ssl.StaticKeyManager

alias(String) - Static method in class net.sf.basedb.core.query.Hql

Same as property(alias, null).

ALIAS_REGEXP - Static variable in class net.sf.basedb.core.query.Hql

An alias can only contain the characters a-z, A-Z or 0-9.

ALIAS_REGEXP - Static variable in class net.sf.basedb.core.query.Selects

An alias can only contain the characters a-z, A-Z or 0-9.

aliasMapping - Static variable in enum class net.sf.basedb.core.Item

ALIGNED_SEQUENCE - Static variable in class net.sf.basedb.core.File

The id for the FileType item representing a file containing aligned sequence data.

ALIGNMENT - Static variable in class net.sf.basedb.core.Protocol

The ID for the alignment protocol type, for example a protocol used when creating a DerivedBioAssay representing data that has been aligned against a reference genome.

ALIGNMENT - Static variable in class net.sf.basedb.core.Software

The id for the SoftwareType item representing software used for aligning sequenced data against a known reference database.

all - Static variable in class net.sf.basedb.core.RawDataTypes

all - Variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset

all(Query) - Static method in class net.sf.basedb.core.query.Expressions

Create a subquery expression: ANY (subquery).

ALL - Enum constant in enum class net.sf.basedb.util.overview.node.ChildNodeDirection

ALL - Static variable in enum class net.sf.basedb.core.Include

A non-modifable collection containing all options.

ALL - Static variable in class net.sf.basedb.core.Keyring

ALL_ITEM - Static variable in class net.sf.basedb.core.Keyring

allCharsets - Static variable in class net.sf.basedb.core.Config

allChildExtractsInChain - Variable in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper

allColumnMappings - Variable in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter

allColumnMappings - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter

allColumnMappings - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

allColumnMappings - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

allColumnMappings - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

allData - Variable in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor

AllEventsFilter - Class in net.sf.basedb.util.extensions.events

Event filter that passes all events.

AllEventsFilter() - Constructor for class net.sf.basedb.util.extensions.events.AllEventsFilter

Create a event type filter that passes all events.

allInsertBatchers - Variable in class net.sf.basedb.core.AnnotationBatcher

allInsertBatchers - Variable in class net.sf.basedb.core.MigrateRbaToDba

allModified - Variable in class net.sf.basedb.core.DerivedBioAssay.FixDerivedBioAssayParentsRecursivelyAction

allMustPass - Variable in class net.sf.basedb.util.extensions.events.CombiningEventFilter

allNodes - Variable in class net.sf.basedb.util.overview.GenericOverview

allObjects - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile

AllOfFilter<T> - Class in net.sf.basedb.util.filter

A filter implementation that accpets an object if all parent filters accepts it.

AllOfFilter(Collection<? extends Filter<? super T>>) - Constructor for class net.sf.basedb.util.filter.AllOfFilter

Create a new filter.

allow - Variable in class net.sf.basedb.core.signal.SocketSignalReceiver

ALLOW_ROOT_NODE - Static variable in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader

allowAll - Variable in class net.sf.basedb.core.signal.SocketSignalReceiver

AllowAnyHostNameVerifyer - Class in net.sf.basedb.util.ssl

A simple implementation of a host name verifyer that allows all hosts.

AllowAnyHostNameVerifyer() - Constructor for class net.sf.basedb.util.ssl.AllowAnyHostNameVerifyer

allowAsRootNode - Variable in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader

allowColumnDrag() - Method in class net.sf.basedb.clients.web.taglib.table.Table

Can header columns be dragged for re-ordering?

allowDoublingBack - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

allowedClients - Variable in class net.sf.basedb.core.SessionControl

allowForward - Variable in class net.sf.basedb.core.signal.SocketSignalReceiver

allowImmediateDownload - Variable in class net.sf.basedb.core.PluginResponse

allowImmediateExecution - Variable in class net.sf.basedb.core.data.PluginDefinitionData

allowImmediateExecution - Variable in class net.sf.basedb.core.PluginConfigurationRequest

allowImmediateExecution - Variable in class net.sf.basedb.core.PluginRequest.RequestImpl

allowImmediateExecution - Variable in class net.sf.basedb.core.PluginResponse

allowMultiple - Variable in class net.sf.basedb.util.timer.ThreadTimerTask

allowRemotePause - Variable in class net.sf.basedb.clients.jobagent.Agent

allowRemoteStart - Variable in class net.sf.basedb.clients.jobagent.Agent

allowRemoteStop - Variable in class net.sf.basedb.clients.jobagent.Agent

allowRendererOverride - Variable in class net.sf.basedb.util.extensions.ExtensionPointBean

allowRendererOverride - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint

allowRendererOverride() - Method in interface net.sf.basedb.util.extensions.ExtensionPoint

If an extension is allowed to override the renderer factory with an implementation of its own.

allowRendererOverride() - Method in class net.sf.basedb.util.extensions.ExtensionPointBean

allowRendererOverride() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint

allowSaveParameters - Variable in enum class net.sf.basedb.core.plugin.Response.Status

allowSaveParameters() - Method in enum class net.sf.basedb.core.plugin.Response.Status

allowSubclass - Variable in class net.sf.basedb.util.filter.InstanceOfFilter

allowUnmodified - Variable in class net.sf.basedb.util.extensions.manager.filter.ValidAndNewOrModifiedFilter

allowUse - Variable in class net.sf.basedb.util.jep.RawFunction

allProjects - Variable in class net.sf.basedb.core.snapshot.SnapshotManager

allProperties - Static variable in class net.sf.basedb.core.ExtendedProperties

A map from class name --> a list of extended properties of for that class.

allSame(Collection<Set<Permission>>) - Static method in class net.sf.basedb.core.MultiPermissions

Check if a collection of Set:s all contain the same permissions.

allSeries - Variable in class net.sf.basedb.util.plot.ScatterPlot

allSql - Variable in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget

allSubContexts - Variable in class net.sf.basedb.clients.web.taglib.table.PresetSelector

If true, presets for all subcontexts are included in the preset, otherwise only presets for the current subcontext (default).

allUpdateBatchers - Variable in class net.sf.basedb.core.AnnotationBatcher

allUpdateBatchers - Variable in class net.sf.basedb.core.MigrateRbaToDba

allVisible - Variable in class net.sf.basedb.clients.web.taglib.table.Table

"all" was specified for the columns attribute.

alphaToNumeric(String) - Static method in class net.sf.basedb.util.Coordinate

Convert an alphanumeric coordinate to a numeric coordinate, case is unimportent.

AlreadyLoggedInException - Exception in net.sf.basedb.core

This exception is thrown if you try to log in but are already logged in.

AlreadyLoggedInException(String) - Constructor for exception net.sf.basedb.core.AlreadyLoggedInException

Creates a new AlreadyLoggedInException.

ALTERNATE_PATH_MATCH - Static variable in class net.sf.basedb.clients.web.servlet.ExtensionsServlet

Alternatively the servlet is: /extensions/servlet and pathInfo is: /[jar-file-name]/[servlet-name]/optional/path/info

alwaysGranted - Variable in class net.sf.basedb.core.plugin.Permissions

AMP - Static variable in class net.sf.basedb.clients.web.util.HTML

AMPERSAND - Static variable in class net.sf.basedb.clients.web.util.HTML

AnalysisFilterPlugin - Interface in net.sf.basedb.core.plugin

This is a tagging interface that should be used by all analysis plug-ins that are filtering data only.

ANALYZE - Enum constant in enum class net.sf.basedb.core.plugin.Plugin.MainType

analyzeAfterBatchOperation() - Method in interface net.sf.basedb.core.dbengine.DbEngine

If TRUE, a batcher that inserts, updates or delets a lot of rows in a table should execute the SQL returned by DbEngine.getAnalyzeTableSql(String, String, String) for that table.

analyzeAfterBatchOperation() - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine

Return false.

analyzeAfterBatchOperation() - Method in class net.sf.basedb.core.dbengine.MySQLEngine

Return true.

analyzeAfterBatchOperation() - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine

Return true.

analyzeAfterImport - Variable in class net.sf.basedb.core.Migration

analyzeTable(String, String, String) - Method in class net.sf.basedb.core.AbstractBatcher

Update index statistics for a table.

analyzeUserAgent(String) - Static method in class net.sf.basedb.util.HttpUtil

Parse the User-Agent string from a HTTP request and return information about what it actually means.

and(Restriction...) - Static method in class net.sf.basedb.core.query.Restrictions

Combine one or more restrictions with AND: new restriction = r[0] AND r[1] AND ...

AND - Enum constant in enum class net.sf.basedb.core.Operator

AndConverter - Class in net.sf.basedb.util.jep.convert

Convert the '&&' operator to a Query API Restriction.

AndConverter() - Constructor for class net.sf.basedb.util.jep.convert.AndConverter

AndRestriction - Class in net.sf.basedb.core.query

Combine one or more restrictions with AND: r[0] AND r[1] AND ...

AndRestriction(Restriction...) - Constructor for class net.sf.basedb.core.query.AndRestriction

ANGLE - Static variable in class net.sf.basedb.core.Quantity

The id for the Quantity object representing angle.

Annotatable - Interface in net.sf.basedb.core

This interface is implemented by all items which can be annotated.

ANNOTATABLE_FILTER - Static variable in class net.sf.basedb.core.QueryRuntimeFilterFactory

AnnotatableData - Interface in net.sf.basedb.core.data

An annotatable item is an item that can be annotated with name/value pairs.

AnnotatableFilter() - Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.AnnotatableFilter

annotatableItems - Static variable in class net.sf.basedb.core.Metadata

AnnotatableProxy - Interface in net.sf.basedb.core

This interface is implemented by items that can be used to hold annotations that are intended for other items.

AnnotatableWrapper(Annotatable, AnnotationUtil.AnnotatableWrapper) - Constructor for class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper

AnnotatableWrapper(Annotatable, AnnotationUtil.Cache) - Constructor for class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper

ANNOTATED - Enum constant in enum class net.sf.basedb.core.Include

Include items that have at least one annotation.

AnnotatedData - Class in net.sf.basedb.core.data

This class extends the CommonData class and implements the AnnotatableData interface.

AnnotatedData() - Constructor for class net.sf.basedb.core.data.AnnotatedData

AnnotatedItem - Class in net.sf.basedb.core

This is a helper class for items that need to implement the Annotatable interface.

AnnotatedItem(AnnotatedData) - Constructor for class net.sf.basedb.core.AnnotatedItem

annotation - Variable in class net.sf.basedb.util.overview.Fix

annotation(AnnotationType, String, Formatter<?>) - Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory

Create an annotation assay field, overriding the title of the annotation type.

annotation(AnnotationType, Formatter<?>) - Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory

Create an annotation assay field.

Annotation - Class in net.sf.basedb.core

This class represents an annotation.

Annotation(AnnotationData) - Constructor for class net.sf.basedb.core.Annotation

Annotation(AnnotationData, AnnotationSet) - Constructor for class net.sf.basedb.core.Annotation

ANNOTATION - Enum constant in enum class net.sf.basedb.core.Item

The item is an Annotation.

ANNOTATION - Enum constant in enum class net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType

ANNOTATION_CLONE_OUTOFSYNC - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if a cloned annotation value is in sync with the source annotation.

ANNOTATION_CLONED_FROM_UNKNOWNPARENT - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if a cloned annotation value has lost the reference to the parent item.

ANNOTATION_INHERIT_FROM_DENIEDPARENT - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if the logged in user has access to the parent item of an inherited annotation value.

ANNOTATION_INHERIT_FROM_NONPARENT - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if an inherited annotation value is inherited from a parent item.

ANNOTATION_INHERIT_MULTIPLE - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if two or more inherited annotations have the same annotation type.

ANNOTATION_INVALID_ITEM - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if an annotation is not valid for the current item type.

ANNOTATION_INVALID_VALUE - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if an annotation value is invalid according to annotation type specification.

ANNOTATION_IS_PARAMETER - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if an annotation is a protocol parameter.

ANNOTATION_TOO_MANY_VALUES - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if an annotation have more values than what the 'multiplicity' setting for the annotation type allow.

Annotation.QueryRuntimeFilterImpl - Class in net.sf.basedb.core

Annotation.Source - Enum Class in net.sf.basedb.core

The annotation source.

AnnotationAssayField - Class in net.sf.basedb.util.export.spotdata

Assay field implementation that exports the annotations of a bioassay.

AnnotationAssayField() - Constructor for class net.sf.basedb.util.export.spotdata.AnnotationAssayField

Create a new annotation field.

AnnotationBatcher - Class in net.sf.basedb.core

Batcher implementation for adding, updating and removing multiple annotations to a large number of items in a single transaction while keeping the memory usage as low as possible.

AnnotationBatcher(DbControl, Item) - Constructor for class net.sf.basedb.core.AnnotationBatcher

Create a new batcher instance.

AnnotationBatcher(DbControl, Item, Integer) - Constructor for class net.sf.basedb.core.AnnotationBatcher

Create a new batcher instance.

AnnotationBatcher(DbControl, Item, Project) - Constructor for class net.sf.basedb.core.AnnotationBatcher

Create a new batcher instance.

AnnotationBatcher.Change - Enum Class in net.sf.basedb.core

A flag indicating what type of change that was made to an annotation as a result of calling AnnotationBatcher.setValues(AnnotationType, List, Unit, boolean)

AnnotationBatcher.CurrentAnnotationInfo - Class in net.sf.basedb.core

Holds information about an annotation for the current item.

AnnotationBatcher.InsertBatcher - Class in net.sf.basedb.core

Batcher implementation for inserting into tables.

AnnotationBatcher.UpdateBatcher - Class in net.sf.basedb.core

Batcher implementation for updating and deleting from tables.

AnnotationBetweenRestriction - Class in net.sf.basedb.core

Restricts a query using annotation values between a low and high value.

AnnotationBetweenRestriction(String, int, Type, Object, Object, boolean, boolean) - Constructor for class net.sf.basedb.core.AnnotationBetweenRestriction

Deprecated.

In 3.11, use AnnotationBetweenRestriction(String, AnnotationType, Object, Object, AnnotationRestriction.Options) instead

AnnotationBetweenRestriction(String, AnnotationType, Object, Object, boolean, boolean) - Constructor for class net.sf.basedb.core.AnnotationBetweenRestriction

Deprecated.

In 3.11, use AnnotationBetweenRestriction(String, AnnotationType, Object, Object, AnnotationRestriction.Options) instead

AnnotationBetweenRestriction(String, AnnotationType, Object, Object, AnnotationRestriction.Options) - Constructor for class net.sf.basedb.core.AnnotationBetweenRestriction

Create a new annotation restriction.

AnnotationData - Class in net.sf.basedb.core.data

This class holds information about an annotation

AnnotationData() - Constructor for class net.sf.basedb.core.data.AnnotationData

AnnotationExpression - Class in net.sf.basedb.core.query

An expression representing the value of an annotation.

AnnotationExpression(String, AnnotationType) - Constructor for class net.sf.basedb.core.query.AnnotationExpression

AnnotationFilter - Class in net.sf.basedb.core.snapshot

Filter implementation that finds the annotation snapshot for a given annotation.

AnnotationFilter() - Constructor for class net.sf.basedb.core.snapshot.AnnotationFilter

Create a filter that matches all annotations.

AnnotationFilter(Annotation) - Constructor for class net.sf.basedb.core.snapshot.AnnotationFilter

Create a filter that matches a specfic annotation.

AnnotationFlatFileImporter - Class in net.sf.basedb.plugins

Plug-in for importing annotations from simple text files.

AnnotationFlatFileImporter() - Constructor for class net.sf.basedb.plugins.AnnotationFlatFileImporter

AnnotationFlatFileImporter.AnnotationValue - Class in net.sf.basedb.plugins

AnnotationFlatFileImporter.NewAnnotations - Class in net.sf.basedb.plugins

Internal cache for storing annotation values from the file for a single item.

AnnotationGroup(int, Set<T>, int, Formatter<T>) - Constructor for class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup

annotationId - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

annotationId - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo

annotationId - Variable in class net.sf.basedb.core.FastAnnotationLoader.FastAnnotation

The ID of the annotation.

annotationId - Variable in class net.sf.basedb.core.snapshot.AnnotationFilter

annotationId - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot

AnnotationIdMethod - Class in net.sf.basedb.plugins.batchimport

Identification method implementation that can use an annotation for identifying items.

AnnotationIdMethod(AnnotationType) - Constructor for class net.sf.basedb.plugins.batchimport.AnnotationIdMethod

Create a new id method.

AnnotationInfo(int, int, int, int) - Constructor for class net.sf.basedb.core.ProjectSpecificAnnotationsManager.AnnotationInfo

AnnotationInfo(int, int, int, int, int, int) - Constructor for class net.sf.basedb.core.ProjectSpecificAnnotationsManager.AnnotationInfo

AnnotationInRestriction - Class in net.sf.basedb.core

Restricts a query using annotation values that exists in a set of given values.

AnnotationInRestriction(String, AnnotationType, boolean, boolean, Object...) - Constructor for class net.sf.basedb.core.AnnotationInRestriction

Deprecated.

In 3.11, use AnnotationInRestriction(String, AnnotationType, AnnotationRestriction.Options, Object...) instead

AnnotationInRestriction(String, AnnotationType, AnnotationRestriction.Options, Object...) - Constructor for class net.sf.basedb.core.AnnotationInRestriction

Create a new annotation restriction.

AnnotationJoin - Class in net.sf.basedb.core.query

Join annotations values to the query.

AnnotationJoin(JoinType, String, AnnotationType, String) - Constructor for class net.sf.basedb.core.query.AnnotationJoin

AnnotationJoiner(JoinType) - Constructor for class net.sf.basedb.core.HqlQueryJoiners.AnnotationJoiner

AnnotationLink - Class in net.sf.basedb.core.data.annotations

Class for mapping the "Annotations" table with shortcuts to all 'FooValues' tables.

AnnotationLink() - Constructor for class net.sf.basedb.core.data.annotations.AnnotationLink

AnnotationLoader - Class in net.sf.basedb.util.overview.loader

Node loader implementation for annotations.

AnnotationLoader() - Constructor for class net.sf.basedb.util.overview.loader.AnnotationLoader

AnnotationLoaderUtil - Class in net.sf.basedb.core.snapshot

Utility implementation for simple loading of primary annotations via SnapshotManager.

AnnotationLoaderUtil(DbControl, SnapshotManager, AnnotationType) - Constructor for class net.sf.basedb.core.snapshot.AnnotationLoaderUtil

Create a loder that uses the given snapshot manager to load annotations for a single annotation type.

AnnotationLoaderUtil(DbControl, SnapshotManager, AnnotationType, boolean, boolean) - Constructor for class net.sf.basedb.core.snapshot.AnnotationLoaderUtil

Create a loder that uses the given snapshot manager to load annotations for a single annotation type.

AnnotationLogger - Class in net.sf.basedb.core.log.db

Logger for annotations that logs changes as updates to the parent item the annotations belong to.

AnnotationLogger(DbLogManagerFactory) - Constructor for class net.sf.basedb.core.log.db.AnnotationLogger

AnnotationModel - Class in net.sf.basedb.util.bfs

A model container for BFS annotation files.

AnnotationModel() - Constructor for class net.sf.basedb.util.bfs.AnnotationModel

Create a new annotation model.

AnnotationNameGenerator - Class in net.sf.basedb.util.overview.node

Since an Annotation isn't Nameable we construct the name from the name of the annotation type, or from the value type if we are not allowed to access the annotation type.

AnnotationNameGenerator() - Constructor for class net.sf.basedb.util.overview.node.AnnotationNameGenerator

AnnotationParser - Class in net.sf.basedb.util.bfs

Parser implementation that parses a BFS annotation files.

AnnotationParser() - Constructor for class net.sf.basedb.util.bfs.AnnotationParser

Create a new annotation parser.

AnnotationRestriction - Class in net.sf.basedb.core

Base class for creating restrictions based on annotations.

AnnotationRestriction(String, int, Type, AnnotationRestriction.Options) - Constructor for class net.sf.basedb.core.AnnotationRestriction

Deprecated.

In 3.11

AnnotationRestriction(String, AnnotationType, AnnotationRestriction.Options) - Constructor for class net.sf.basedb.core.AnnotationRestriction

Create a new annotation restriction for an annotation type.

AnnotationRestriction.Options - Class in net.sf.basedb.core

Options that specify which annotations to consider when searching.

annotations - Variable in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey

annotations - Variable in class net.sf.basedb.core.data.AnnotationSetData

annotations - Variable in class net.sf.basedb.core.data.AnnotationTypeData

annotations - Variable in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot

Annotations - Class in net.sf.basedb.core.query

A factory class to create restrictions based on annotation values.

Annotations() - Constructor for class net.sf.basedb.core.query.Annotations

annotationSection - Static variable in class net.sf.basedb.core.plugin.AbstractPlugin

Section definition for grouping annotation options.

annotationSet - Variable in class net.sf.basedb.core.Annotation

annotationSet - Variable in class net.sf.basedb.core.data.AnnotatedData

annotationSet - Variable in class net.sf.basedb.core.data.AnnotationData

annotationSet - Variable in class net.sf.basedb.core.data.BioAssayData

annotationSet - Variable in class net.sf.basedb.core.data.BioAssaySetData

annotationSet - Variable in class net.sf.basedb.core.data.PluginDefinitionData

annotationSet - Variable in class net.sf.basedb.core.data.ProjectData

annotationSet - Variable in class net.sf.basedb.core.data.RootRawBioAssayData

annotationSet - Variable in class net.sf.basedb.core.data.WellData

annotationSet - Variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager.AnnotationInfo

annotationSet - Variable in class net.sf.basedb.util.overview.validator.ProtocolParameterValidator

AnnotationSet - Class in net.sf.basedb.core

An annotation set is the container for all annotations on an item.

AnnotationSet(AnnotationSetData) - Constructor for class net.sf.basedb.core.AnnotationSet

Regular constructor if the item is not known beforehand.

AnnotationSet(AnnotationSetData, Annotatable) - Constructor for class net.sf.basedb.core.AnnotationSet

Special constructor to avoid AnnotationSet.getItem() to hit the database when the item is known beforehand.

ANNOTATIONSET - Enum constant in enum class net.sf.basedb.core.Item

The item is an AnnotationSet.

AnnotationSet.ProjectSpecificAnnotationsRestriction - Class in net.sf.basedb.core

Restriction for matching project-specific annotations against the currently active project.

AnnotationSet.QueryRuntimeFilterImpl - Class in net.sf.basedb.core

AnnotationSetData - Class in net.sf.basedb.core.data

This class holds information about a set of annotations.

AnnotationSetData() - Constructor for class net.sf.basedb.core.data.AnnotationSetData

annotationSetId - Variable in class net.sf.basedb.core.AnnotationSet.ProjectSpecificAnnotationsRestriction

annotationSetId - Variable in class net.sf.basedb.core.data.annotations.AnnotationLink

annotationSetId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba

annotationSetId - Variable in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot

annotationSetId - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot

AnnotationSetLogger - Class in net.sf.basedb.core.log.db

Logger for annotations sets that detects and logs changes to inherited anntations as updates to the parent item that are inheriting the annotations.

AnnotationSetLogger(DbLogManagerFactory) - Constructor for class net.sf.basedb.core.log.db.AnnotationSetLogger

AnnotationSetSnapshot - Class in net.sf.basedb.core.snapshot

A snapshot of an annotation set that is used to store information as a file.

AnnotationSetSnapshot() - Constructor for class net.sf.basedb.core.snapshot.AnnotationSetSnapshot

Creates a new, empty snapshot.

AnnotationSetSnapshot.SortByProjectComparator - Class in net.sf.basedb.core.snapshot

Comparator for sorting annotation snapshots so that project-specific annotations appear before default annotations.

AnnotationSetterPlugin - Interface in net.sf.basedb.core.plugin

This is a interface that should be implemented by plug-ins that are setting annotations on items thy create or work with.

AnnotationSimpleRestriction - Class in net.sf.basedb.core

Restricts a query using annotation values with a simple expression: annotation operator value.

AnnotationSimpleRestriction(String, int, Type, Operator, Object, boolean, boolean) - Constructor for class net.sf.basedb.core.AnnotationSimpleRestriction

Deprecated.

In 3.11, use AnnotationSimpleRestriction(String, AnnotationType, Operator, Object, AnnotationRestriction.Options) instead

AnnotationSimpleRestriction(String, int, Type, Operator, List<Object>, boolean, boolean) - Constructor for class net.sf.basedb.core.AnnotationSimpleRestriction

Deprecated.

In 3.11, use AnnotationSimpleRestriction(String, AnnotationType, Operator, List, AnnotationRestriction.Options) instead

AnnotationSimpleRestriction(String, AnnotationType, Operator, Object, boolean, boolean) - Constructor for class net.sf.basedb.core.AnnotationSimpleRestriction

Deprecated.

In 3.11, use AnnotationSimpleRestriction(String, AnnotationType, Operator, Object, AnnotationRestriction.Options) instead

AnnotationSimpleRestriction(String, AnnotationType, Operator, Object, AnnotationRestriction.Options) - Constructor for class net.sf.basedb.core.AnnotationSimpleRestriction

Create a new annotation restriction using a simple expression: annotation operator value.

AnnotationSimpleRestriction(String, AnnotationType, Operator, List<Object>, AnnotationRestriction.Options) - Constructor for class net.sf.basedb.core.AnnotationSimpleRestriction

Creates a new annotation restriction for a specific valueType.

AnnotationSnapshot - Class in net.sf.basedb.core.snapshot

Stores information about a single primary or inherited annotation or an inherited annotation set.

AnnotationSnapshot() - Constructor for class net.sf.basedb.core.snapshot.AnnotationSnapshot

Create a new, empty annotation snapshot.

AnnotationSnapshot.AnnotationTypeComparator - Class in net.sf.basedb.core.snapshot

Comparator implementation for sorting snapshots by name of annotation type.

AnnotationSnapshot.ProjectComparator - Class in net.sf.basedb.core.snapshot

Comparator implementation for sorting snapshots by name of project.

AnnotationSummary(ExperimentExplorer, DbControl, AnnotationType) - Constructor for class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary

annotationType - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary

annotationType - Variable in class net.sf.basedb.clients.web.plugins.ExportedProperty

annotationType - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo

annotationType - Variable in class net.sf.basedb.core.AnnotationRestriction

annotationType - Variable in class net.sf.basedb.core.data.AnnotationData

annotationType - Variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager.AnnotationInfo

annotationType - Variable in class net.sf.basedb.core.query.AnnotationExpression

annotationType - Variable in class net.sf.basedb.core.query.AnnotationJoin

annotationType - Variable in class net.sf.basedb.plugins.batchimport.AnnotationIdMethod

annotationType - Variable in class net.sf.basedb.util.annotations.InheritSpecification

annotationType - Variable in class net.sf.basedb.util.overview.Fix

AnnotationType - Class in net.sf.basedb.core

Objects of this class defines an annotation type.

AnnotationType(AnnotationTypeData) - Constructor for class net.sf.basedb.core.AnnotationType

ANNOTATIONTYPE - Enum constant in enum class net.sf.basedb.core.Item

The item is an AnnotationType.

AnnotationType.RemoveInheritedAnnotationsAction - Class in net.sf.basedb.core

AnnotationTypeCategory - Class in net.sf.basedb.core

Objects of this class defines an annotation type category.

AnnotationTypeCategory(AnnotationTypeCategoryData) - Constructor for class net.sf.basedb.core.AnnotationTypeCategory

ANNOTATIONTYPECATEGORY - Enum constant in enum class net.sf.basedb.core.Item

The item is an AnnotationTypeCategory.

AnnotationTypeCategoryData - Class in net.sf.basedb.core.data

This data layer class holds information about annotation type categories.

AnnotationTypeCategoryData() - Constructor for class net.sf.basedb.core.data.AnnotationTypeCategoryData

annotationTypeCategoryQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

AnnotationTypeComparator(DbControl) - Constructor for class net.sf.basedb.core.snapshot.AnnotationSnapshot.AnnotationTypeComparator

AnnotationTypeData - Class in net.sf.basedb.core.data

This class holds information about an annotation type.

AnnotationTypeData() - Constructor for class net.sf.basedb.core.data.AnnotationTypeData

AnnotationTypeEnumerationLoader - Class in net.sf.basedb.clients.web.plugins

Data loader implementation for loading the enumeration values collection of an annotation type.

AnnotationTypeEnumerationLoader() - Constructor for class net.sf.basedb.clients.web.plugins.AnnotationTypeEnumerationLoader

AnnotationTypeFilter - Class in net.sf.basedb.core.snapshot

Filter implementation that finds all annotation snapshots for a given annotation type.

AnnotationTypeFilter() - Constructor for class net.sf.basedb.core.snapshot.AnnotationTypeFilter

Create a filter that matches all annotation types.

AnnotationTypeFilter(Annotation.Source) - Constructor for class net.sf.basedb.util.annotations.InheritAnnotationsManager.AnnotationTypeFilter

AnnotationTypeFilter(AnnotationType) - Constructor for class net.sf.basedb.core.snapshot.AnnotationTypeFilter

Create a filter that matches a specfic annotation type.

annotationTypeId - Variable in class net.sf.basedb.core.AnnotationRestriction

annotationTypeId - Variable in class net.sf.basedb.core.data.annotations.AnnotationLink

annotationTypeId - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot

annotationTypeId - Variable in class net.sf.basedb.core.snapshot.AnnotationTypeFilter

annotationTypeId - Variable in class net.sf.basedb.util.annotations.InheritSpecification

annotationTypeIds - Variable in class net.sf.basedb.clients.web.ExperimentExplorer

The currently selected annotation types on the view page.

annotationTypeIds - Variable in class net.sf.basedb.core.Annotation.QueryRuntimeFilterImpl

AnnotationTypeImporter - Class in net.sf.basedb.plugins.batchimport

Plug-in for importing annotation type items in a batch.

AnnotationTypeImporter() - Constructor for class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

AnnotationTypeItemTypesLoader - Class in net.sf.basedb.clients.web.plugins

Data loader implementation for loading the item types collection of an annotation type.

AnnotationTypeItemTypesLoader() - Constructor for class net.sf.basedb.clients.web.plugins.AnnotationTypeItemTypesLoader

annotationTypes - Variable in class net.sf.basedb.core.data.AnnotationTypeCategoryData

annotationTypes - Variable in class net.sf.basedb.util.annotations.InheritAnnotationsManager.AnnotationTypeFilter

annotationTypeSection - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

Section definition for grouping all mappings of columns to annotation types.

AnnotationUtil - Class in net.sf.basedb.clients.web

Some utility functions for annotations.

AnnotationUtil - Class in net.sf.basedb.util

Utility class for working with annotations.

AnnotationUtil() - Constructor for class net.sf.basedb.clients.web.AnnotationUtil

AnnotationUtil() - Constructor for class net.sf.basedb.util.AnnotationUtil

AnnotationUtil.AnnotatableWrapper - Class in net.sf.basedb.util

This wrapper class is needed because we need to keep track of extracts linked with raw bioassays and derived bioassays until we have loaded the Extracts of a Physical Bioassay.

AnnotationUtil.Cache - Class in net.sf.basedb.util

AnnotationValidator - Class in net.sf.basedb.util.overview.validator

Validator implementation for annotations.

AnnotationValidator() - Constructor for class net.sf.basedb.util.overview.validator.AnnotationValidator

AnnotationValue(Object, Unit) - Constructor for class net.sf.basedb.plugins.AnnotationFlatFileImporter.AnnotationValue

annotationValues - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup

AnnotationWriter - Class in net.sf.basedb.util.bfs

AnnotationWriter(Writer) - Constructor for class net.sf.basedb.util.bfs.AnnotationWriter

any - Variable in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext

any(Query) - Static method in class net.sf.basedb.core.query.Expressions

Create a subquery expression: ANY (subquery).

ANY_TO_ANY - Enum constant in enum class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext.Type

The context is a list with any-to-any links from a parent item.

AnyLinkColumn - Class in net.sf.basedb.clients.web.extensions.list

A column action implementation that finds an item linked with a any-to-any link.

AnyLinkColumn(int, String, String, Item, Metadata.PropertyPath<BasicItem, ?>, FileViewerUtil) - Constructor for class net.sf.basedb.clients.web.extensions.list.AnyLinkColumn

AnyLinkColumnActionFactory - Class in net.sf.basedb.clients.web.extensions.list

Action factory for adding columns to a table that display items that are linked with an any-to-any link.

AnyLinkColumnActionFactory() - Constructor for class net.sf.basedb.clients.web.extensions.list.AnyLinkColumnActionFactory

anyToAny(BasicItem) - Static method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext

Creates an any-to-any listing context where files belong to a parent item.

AnyToAny - Class in net.sf.basedb.core

An any-to-any link is a named, directed link from one item to another item.

AnyToAny(AnyToAnyData) - Constructor for class net.sf.basedb.core.AnyToAny

Creates a new link item from the given data.

AnyToAny(AnyToAnyData, BasicItem) - Constructor for class net.sf.basedb.core.AnyToAny

Special constructor when the from item is known.

ANYTOANY - Enum constant in enum class net.sf.basedb.core.Item

The item is an AnyToAny link.

AnyToAny.FastLinkLoader<S extends BasicItem,T extends BasicItem> - Class in net.sf.basedb.core

Helper class for faster loading of any-to-any links between items.

AnyToAnyData - Class in net.sf.basedb.core.data

Represents a link from one item to any other item.

AnyToAnyData() - Constructor for class net.sf.basedb.core.data.AnyToAnyData

AnyToAnyDataLoader - Class in net.sf.basedb.clients.web.plugins

Data loader implementation that load any-to-any links.

AnyToAnyDataLoader(String, Item, Metadata.PropertyPath<BasicItem, ?>) - Constructor for class net.sf.basedb.clients.web.plugins.AnyToAnyDataLoader

Load links with the specified name and target type.

AnyToAnyImporter - Class in net.sf.basedb.plugins.batchimport

Plug-in for importing any-to-any links from simple text files.

AnyToAnyImporter() - Constructor for class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

AnyToAnyLinkStatistics - Class in net.sf.basedb.util

Class for holding statisics about any-to-any links between items.

AnyToAnyLinkStatistics() - Constructor for class net.sf.basedb.util.AnyToAnyLinkStatistics

AnyToAnyLinkStatistics.Options - Class in net.sf.basedb.util

Options to specify how the statistics should be generated.

AnyToAnyLoader - Class in net.sf.basedb.util.overview.loader

Node loader implementation for any-to-any links.

AnyToAnyLoader() - Constructor for class net.sf.basedb.util.overview.loader.AnyToAnyLoader

AnyToAnyLogger - Class in net.sf.basedb.core.log.db

Logger for any-to-any links that logs changes as updates to the 'from' item.

AnyToAnyLogger(DbLogManagerFactory) - Constructor for class net.sf.basedb.core.log.db.AnyToAnyLogger

AnyToAnyNameGenerator - Class in net.sf.basedb.util.overview.node

Name generator for any-to-any links.

AnyToAnyNameGenerator() - Constructor for class net.sf.basedb.util.overview.node.AnyToAnyNameGenerator

AnyToAnyRestriction - Class in net.sf.basedb.core.query

Expression that can be used to filter on the existence or non-existence of a named any-to-any link.

AnyToAnyRestriction(String, String, Item, boolean, EntityQuery) - Constructor for class net.sf.basedb.core.query.AnyToAnyRestriction

AnyToAnyValidator - Class in net.sf.basedb.util.overview.validator

Validator implementation for any-to-any links.

AnyToAnyValidator() - Constructor for class net.sf.basedb.util.overview.validator.AnyToAnyValidator

append(String) - Method in class net.sf.basedb.core.Job.ProgressReporterImpl

append(String) - Method in class net.sf.basedb.core.Migration.ProgressInputStream

append(String) - Method in interface net.sf.basedb.core.ProgressReporter

Append a message to the previous one.

append(String) - Method in class net.sf.basedb.core.signal.ProgressReporterSignalHandler

append(String) - Method in class net.sf.basedb.core.SimpleProgressReporter

append(String) - Method in class net.sf.basedb.util.ChainedProgressReporter

append(String) - Method in class net.sf.basedb.util.ConsoleProgressReporter

append(String) - Method in class net.sf.basedb.util.GeoLocation.ResponseFilter

append(String) - Method in class net.sf.basedb.util.TransferRateProgressReporter

Forward the call to the parent if one exists.

append(StringBuilder, String) - Method in class net.sf.basedb.util.GeoLocation

appendFakeSources(Set<Integer>) - Method in class net.sf.basedb.util.listable.SourceItemTransformerChain

appendGroups(StringBuilder, DbControl, List<Expression>, int) - Method in class net.sf.basedb.core.AbstractQuery

appendHavings(StringBuilder, DbControl, List<Restriction>, int) - Method in class net.sf.basedb.core.AbstractQuery

appendJoins(StringBuilder, DbControl, List<Join>, boolean, int) - Method in class net.sf.basedb.core.AbstractQuery

appendLine(StringBuffer, String[], GtfInputStream.Attribute[]) - Method in class net.sf.basedb.util.gtf.GtfInputStream

Append columns to the buffer and separate each with a tab.

appendList(StringBuilder, Collection<String>) - Method in class net.sf.basedb.core.dbengine.MySQLEngine

appendList(StringBuilder, Collection<String>) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine

appendListOfValues(StringBuilder, String, String) - Method in class net.sf.basedb.util.formatter.PropertyFilterFormatter

appendOrders(StringBuilder, DbControl, List<Order>, int) - Method in class net.sf.basedb.core.AbstractQuery

appendPermissionOption(StringBuilder, Permission, Permission, String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

appendProgress(Session, String) - Method in class net.sf.basedb.core.Job.ProgressReporterImpl

appendRestrictions(StringBuilder, DbControl, List<Restriction>, int) - Method in class net.sf.basedb.core.AbstractQuery

appendScripts(StringBuilder, JspContext) - Method in class net.sf.basedb.clients.web.taglib.Head

appendSelects(StringBuilder, DbControl, List<Select>, int) - Method in class net.sf.basedb.core.AbstractQuery

appendStyles(StringBuilder, String, boolean, JspContext) - Method in class net.sf.basedb.clients.web.taglib.Head

appId - Variable in class net.sf.basedb.core.data.SchemaVersionData

appId - Variable in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration

Application - Class in net.sf.basedb.core

This class represents the BASE application and is the starting point for all client applications.

Application() - Constructor for class net.sf.basedb.core.Application

Application.DbCleaner - Class in net.sf.basedb.core

Application.Pinger - Class in net.sf.basedb.core

A Pinger is an object that is used to protect another object from timing out by automatically pinging it.

Application.SessionControlCacheCleaner - Class in net.sf.basedb.core

Application.StartupOptions - Class in net.sf.basedb.core

Startup optins when starting the BASE application.

apply(List<Plate>, PlateType) - Method in class net.sf.basedb.core.PlateMapping

Apply this mapping to the given list of source plates and generate new plates of the specified type.

applyGraph(RootGraph, GraphSemantic) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

applyToContext(ItemContext) - Method in class net.sf.basedb.clients.web.SubContext

Apply the new subcontext to the given item context.

approximateNumberOfRows - Variable in class net.sf.basedb.core.dbengine.TableInfo

aquireLock(String, boolean, int) - Method in class net.sf.basedb.util.StaticCache

Aquire a read or write lock on a given cache entry.

AREA - Static variable in class net.sf.basedb.core.Quantity

The id for the Quantity object representing area.

ARITHMETIC_MEAN - Enum constant in enum class net.sf.basedb.core.Formula.AverageMethod

arrangeData(int, short, Object[][], Object[]) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter

Arrange the data that was returned by the query into the data writers array.

arrangeData(int, short, Object[][], Object[]) - Method in class net.sf.basedb.util.export.spotdata.MatrixBfsExporter

The column number is used to find the assay index.

arrangeData(int, short, Object[][], Object[]) - Method in class net.sf.basedb.util.export.spotdata.SerialBfsExporter

The column number is used to find the assay index.

ARRANGEMENT - Static variable in class net.sf.basedb.core.DerivedBioAssay

The id for the DerivedBioAssayType item representing sequenced data that has been aligned to a reference database.

array - Variable in class net.sf.basedb.util.ArrayIterator

The array to iterate.

arrayBatch - Variable in class net.sf.basedb.core.data.ArraySlideData

ArrayBatch - Class in net.sf.basedb.core

This class represents the making of a new batch of microarray slides of a particular design.

ArrayBatch(ArrayBatchData) - Constructor for class net.sf.basedb.core.ArrayBatch

ARRAYBATCH - Enum constant in enum class net.sf.basedb.core.Item

The item is an ArrayBatch.

arrayBatchColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.ArraySlideImporter

ArrayBatchData - Class in net.sf.basedb.core.data

This class represents the making of a new batch of microarray slides of a particular design.

ArrayBatchData() - Constructor for class net.sf.basedb.core.data.ArrayBatchData

arrayBatches - Variable in class net.sf.basedb.core.data.ArrayDesignData

ArrayBatchImporter - Class in net.sf.basedb.plugins.batchimport

Plug-in for importing array batch items in a batch.

ArrayBatchImporter() - Constructor for class net.sf.basedb.plugins.batchimport.ArrayBatchImporter

ArrayBatchLoader - Class in net.sf.basedb.util.overview.loader

Node loader implementation for array batches.

ArrayBatchLoader() - Constructor for class net.sf.basedb.util.overview.loader.ArrayBatchLoader

arrayBatchMapper - Variable in class net.sf.basedb.plugins.batchimport.ArraySlideImporter

ArrayBatchValidator - Class in net.sf.basedb.util.overview.validator

Validator implementation for array batch.

ArrayBatchValidator() - Constructor for class net.sf.basedb.util.overview.validator.ArrayBatchValidator

arrayDesign - Variable in class net.sf.basedb.core.data.ArrayBatchData

arrayDesign - Variable in class net.sf.basedb.core.data.ArrayDesignBlockData

arrayDesign - Variable in class net.sf.basedb.core.data.ArrayDesignPlateData

arrayDesign - Variable in class net.sf.basedb.core.data.RawBioAssayData

arrayDesign - Variable in class net.sf.basedb.core.FeatureBatcher

The array design this batcher adds features to.

arrayDesign - Variable in class net.sf.basedb.core.RawDataBatcher

The array design the raw bioassay is connected to, if any.

arrayDesign - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter

arrayDesign - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

ArrayDesign - Class in net.sf.basedb.core

An array design is a description of the design of a microarray slide.

ArrayDesign(ArrayDesignData) - Constructor for class net.sf.basedb.core.ArrayDesign

ARRAYDESIGN - Enum constant in enum class net.sf.basedb.core.Item

The item is an ArrayDesign.

arrayDesignBlock - Variable in class net.sf.basedb.core.data.FeatureData

ArrayDesignBlock - Class in net.sf.basedb.core

ArrayDesignBlock(ArrayDesignBlockData) - Constructor for class net.sf.basedb.core.ArrayDesignBlock

ARRAYDESIGNBLOCK - Enum constant in enum class net.sf.basedb.core.Item

The item is an ArrayDesignBlock.

ArrayDesignBlockData - Class in net.sf.basedb.core.data

This holds information about a block in an arraydesign.

ArrayDesignBlockData() - Constructor for class net.sf.basedb.core.data.ArrayDesignBlockData

arrayDesignBlocks - Variable in class net.sf.basedb.core.data.ArrayDesignData

arrayDesignColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter

arrayDesignColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

arrayDesignData - Variable in class net.sf.basedb.core.FeatureBatcher

Just a copy of the data object for the array design.

ArrayDesignData - Class in net.sf.basedb.core.data

This class holds information about an arrayDesign

ArrayDesignData() - Constructor for class net.sf.basedb.core.data.ArrayDesignData

arrayDesignHasBeenSet - Variable in class net.sf.basedb.core.RawBioAssay

arrayDesignId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba

ArrayDesignImporter - Class in net.sf.basedb.plugins.batchimport

Plug-in for importing array design items in a batch.

ArrayDesignImporter() - Constructor for class net.sf.basedb.plugins.batchimport.ArrayDesignImporter

arrayDesignLinkId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba

ArrayDesignLoader - Class in net.sf.basedb.util.overview.loader

Node loader implementation for array designs.

ArrayDesignLoader() - Constructor for class net.sf.basedb.util.overview.loader.ArrayDesignLoader

arrayDesignMapper - Variable in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter

arrayDesignMapper - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

arrayDesignParameter - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter

arrayDesignParameter - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

ArrayDesignPlate - Class in net.sf.basedb.core

ArrayDesignPlate(ArrayDesignPlateData) - Constructor for class net.sf.basedb.core.ArrayDesignPlate

ARRAYDESIGNPLATE - Enum constant in enum class net.sf.basedb.core.Item

The item is a ArrayDesignPlate connecter.

ArrayDesignPlateData - Class in net.sf.basedb.core.data

This class connects the ArrayDesign with its plates and adding an index to that connection.

ArrayDesignPlateData() - Constructor for class net.sf.basedb.core.data.ArrayDesignPlateData

arrayDesigns - Variable in class net.sf.basedb.core.data.JobData

arrayDesigns - Variable in class net.sf.basedb.core.data.PlateData

arrayDesignType - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter

arrayDesignType - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

ArrayDesignValidator - Class in net.sf.basedb.util.overview.validator

Validator implementation for array designs.

ArrayDesignValidator() - Constructor for class net.sf.basedb.util.overview.validator.ArrayDesignValidator

ArrayIterator<E> - Class in net.sf.basedb.util

This class implements the Iterator interface for an array of objects.

ArrayIterator(E[]) - Constructor for class net.sf.basedb.util.ArrayIterator

Create a new ArrayIterator object.

arraySlide - Variable in class net.sf.basedb.core.data.PhysicalBioAssayData

ArraySlide - Class in net.sf.basedb.core

This class represents a physical microarray slide.

ArraySlide(ArraySlideData) - Constructor for class net.sf.basedb.core.ArraySlide

ARRAYSLIDE - Enum constant in enum class net.sf.basedb.core.Item

The item is an ArraySlide.

arraySlideColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter

ArraySlideData - Class in net.sf.basedb.core.data

This class represents a phycsical microarray slide.

ArraySlideData() - Constructor for class net.sf.basedb.core.data.ArraySlideData

ArraySlideImporter - Class in net.sf.basedb.plugins.batchimport

Plug-in for importing array slide items in a batch.

ArraySlideImporter() - Constructor for class net.sf.basedb.plugins.batchimport.ArraySlideImporter

ArraySlideLoader - Class in net.sf.basedb.util.overview.loader

Node loader implementation for array slides.

ArraySlideLoader() - Constructor for class net.sf.basedb.util.overview.loader.ArraySlideLoader

arraySlideMapper - Variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter

arraySlideQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

arraySlides - Variable in class net.sf.basedb.core.data.ArrayBatchData

ArraySlideValidator - Class in net.sf.basedb.util.overview.validator

Validator implementation for array slides.

ArraySlideValidator() - Constructor for class net.sf.basedb.util.overview.validator.ArraySlideValidator

asBoolean(Boolean) - Static method in class net.sf.basedb.util.excel.ExcelValue

Create a numeric cell value with boolean format.

asc(Expression) - Static method in class net.sf.basedb.core.query.Orders

Sort the result of a query in ascending order by the expression.

ASC - Enum constant in enum class net.sf.basedb.core.ItemContext.SortDirection

Items are sorted in ascending order.

AscOrder - Class in net.sf.basedb.core.query

Sort the result of a query in ascending order by the expression.

AscOrder(Expression) - Constructor for class net.sf.basedb.core.query.AscOrder

asDate - Variable in class net.sf.basedb.util.parser.ConstantMapper

asDate(Date, String) - Static method in class net.sf.basedb.util.excel.ExcelValue

Create a date cell value.

asDouble - Variable in class net.sf.basedb.util.parser.ConstantMapper

asEnumeration(Collection<String>) - Static method in class net.sf.basedb.util.charset.CharsetUtil

Convert charset names to an enumeration with display-friendly key/title pairs.

asInt(Number) - Static method in class net.sf.basedb.util.excel.ExcelValue

Create a numeric cell value without any decimals.

asJsonObject() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

Get a JSON representation of this column definition.

asLong - Variable in class net.sf.basedb.util.parser.ConstantMapper

asNumber(Number, int) - Static method in class net.sf.basedb.util.excel.ExcelValue

Create a numeric cell value and display a given number of decimals.

asNumber(Number, String) - Static method in class net.sf.basedb.util.excel.ExcelValue

Create a numeric cell value with a custom numeric format.

assayAnnotationQuery - Variable in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter

assayField(String, String, Type) - Method in class net.sf.basedb.plugins.BfsExporterPlugin

AssayField - Interface in net.sf.basedb.util.export.spotdata

Represents a bioassay field that is going to be exported.

assayFields - Variable in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

assayFields - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo

assayGroups - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary

assayIndexMap - Variable in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

assayProperty(String, String, Type, Formatter<?>) - Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory

Create a property assay field.

AssayPropertyField - Class in net.sf.basedb.util.export.spotdata

Assay field implementation that exports a named property from a bioassay.

AssayPropertyField() - Constructor for class net.sf.basedb.util.export.spotdata.AssayPropertyField

Create a new annotation field.

assays - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo

assays - Variable in class net.sf.basedb.util.importer.spotdata.MatrixSpotIntensityEventHandler

assays - Variable in class net.sf.basedb.util.importer.spotdata.SerialSpotIntensityEventHandler

assaysHaveParentAssaysMapping - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo

assayWriter - Variable in class net.sf.basedb.util.export.spotdata.BfsExporter

associateFiles(DbControl, Transformation, Directory) - Method in class net.sf.basedb.plugins.Base1PluginExecuter

associationsSection - Static variable in class net.sf.basedb.plugins.IlluminaRawDataImporter

Section definition for grouping associations to other items: scan, software, protocol and experiment

asString(String) - Static method in class net.sf.basedb.util.excel.ExcelValue

Create a string cell value.

ASTConstantConverter - Class in net.sf.basedb.util.jep.convert

Converts a constant node to an expression.

ASTConstantConverter() - Constructor for class net.sf.basedb.util.jep.convert.ASTConstantConverter

ASTFunNodeConverter - Class in net.sf.basedb.util.jep.convert

Converts a function node to an expression or restriction.

ASTFunNodeConverter() - Constructor for class net.sf.basedb.util.jep.convert.ASTFunNodeConverter

asTimestamp(Date, String) - Static method in class net.sf.basedb.util.excel.ExcelValue

Create a timestamp cell value.

ASTVarNodeConverter - Class in net.sf.basedb.util.jep.convert

Converts a variable node to a parameter expression or null.

ASTVarNodeConverter() - Constructor for class net.sf.basedb.util.jep.convert.ASTVarNodeConverter

asXml() - Method in class net.sf.basedb.core.Presets

Convert the presets to an XML string.

at - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemAnnotationColumn

at - Variable in class net.sf.basedb.core.AnnotationType.RemoveInheritedAnnotationsAction

at - Variable in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil

at - Variable in class net.sf.basedb.util.export.spotdata.AnnotationAssayField

AT_OR_DOT - Static variable in class net.sf.basedb.clients.web.util.HTML

atBoundary - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStatus

TRUE if the FileUpload.checkBoundary(byte[], int, byte[], int) method finds that the line matches the boundary, FALSE otherwise.

atCommit - Variable in class net.sf.basedb.core.DropDynamicTableAction

atComp - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot.ProjectComparator

atFilter - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemAnnotationColumn

atId - Variable in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil

atLastBoundary - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStatus

TRUE if the FileUpload.checkBoundary(byte[], int, byte[], int) method finds that the line matches the boundary + two extra dashes (--), FALSE otherwise.

atRollback - Variable in class net.sf.basedb.core.DropDynamicTableAction

attribute - Variable in class net.sf.basedb.util.overview.filter.HasAttributeFilter

Attribute(String, String) - Constructor for class net.sf.basedb.util.gtf.GtfInputStream.Attribute

ATTRIBUTE_KEY - Static variable in class net.sf.basedb.clients.web.extensions.JspContext

The key that is used when storing a JspContext object in a request/page/session/etc. attribute.

ATTRIBUTE_PATTERN - Variable in class net.sf.basedb.util.gtf.GtfInputStream

AttributeKey(String, String) - Constructor for class net.sf.basedb.util.extensions.Registry.AttributeKey

attributes - Variable in class net.sf.basedb.core.authentication.LoginRequest

attributes - Variable in class net.sf.basedb.util.extensions.AboutBean

attributes - Variable in class net.sf.basedb.util.extensions.ClientContext

attributes - Variable in class net.sf.basedb.util.extensions.Registry

attributes - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredAbout

attributes - Variable in class net.sf.basedb.util.gtf.GtfInputStream

attributes - Variable in class net.sf.basedb.util.overview.Node

authenticate() - Method in interface net.sf.basedb.core.authentication.AuthenticationManager

Try to authenticate a user given the login information passed to the factory in the AuthenticationContext.

authenticatedUser - Variable in class net.sf.basedb.core.SessionControl.UnverifiedDeviceInfo

AuthenticatedUser - Class in net.sf.basedb.core.authentication

Objects of this class are returned by the AuthenticationManager.authenticate() method and contains information about the authenticated user.

AuthenticatedUser(AuthenticationMethod, String, String) - Constructor for class net.sf.basedb.core.authentication.AuthenticatedUser

Creates a new AuthenticatedUser object without any link to an existing user in BASE.

AuthenticatedUser(AuthenticationMethod, UserData) - Constructor for class net.sf.basedb.core.authentication.AuthenticatedUser

Creates a new AuthenticatedUser object with a link to an existing user in BASE.

AuthenticationContext - Class in net.sf.basedb.core

Gives authentication implementations limited access to the database.

AuthenticationContext(SessionControl, Session, LoginRequest) - Constructor for class net.sf.basedb.core.AuthenticationContext

AuthenticationException - Exception in net.sf.basedb.core.authentication

This exception can be thrown when an error occurs during the authentication.

AuthenticationException(String) - Constructor for exception net.sf.basedb.core.authentication.AuthenticationException

Create a new AuthenticationException object

AuthenticationException(String, Throwable) - Constructor for exception net.sf.basedb.core.authentication.AuthenticationException

Create a new AuthenticationException object

AuthenticationException(Throwable) - Constructor for exception net.sf.basedb.core.authentication.AuthenticationException

Create a new AuthenticationException object

AuthenticationManager - Interface in net.sf.basedb.core.authentication

Action interface for external authentication.

authenticationMethod - Variable in class net.sf.basedb.core.data.SessionData

authenticationMethod - Variable in class net.sf.basedb.core.SessionControl.LoginInfo

The authentication method used to allow the user to login.

AuthenticationMethod - Class in net.sf.basedb.core.authentication

Holds information about the method that was used to verify a user when logging in.

AuthenticationMethod(String) - Constructor for class net.sf.basedb.core.authentication.AuthenticationMethod

authors - Variable in class net.sf.basedb.core.data.ExperimentData

AUTO - Enum constant in enum class net.sf.basedb.core.ItemContext.AddFilter

Add a filter only if no filter already exists.

AUTO - Enum constant in enum class net.sf.basedb.core.ReporterCloneBatcher.CloneSource

Select VIRTUAL if the experiment has position data in the virtual database, otherwise the RAW options used.

AutoChildNodeLoader<I> - Class in net.sf.basedb.util.overview.loader

Node loader implementation that automatically loads child nodes.

AutoChildNodeLoader(NodeLoader<I>) - Constructor for class net.sf.basedb.util.overview.loader.AutoChildNodeLoader

autoCloseParsers - Variable in class net.sf.basedb.util.importer.spotdata.BfsImporter

autoCloseWriters - Variable in class net.sf.basedb.util.export.spotdata.BaseFileExporter

autoCloseWriters - Variable in class net.sf.basedb.util.export.spotdata.BfsExporter

autoCompress - Variable in class net.sf.basedb.core.data.DirectoryData

autoCompress - Variable in class net.sf.basedb.core.data.MimeTypeData

autoCompressionEnabled() - Static method in class net.sf.basedb.core.Application

Check if auto-compression has been enabled or not.

autoDetect(ExtensionsInvoker<ConnectionManagerFactory>, URI) - Static method in class net.sf.basedb.util.uri.ConnectionManagerUtil

Use auto-detection and return the first factory that can handle the given uri.

AutoDetectFileFormat - Class in net.sf.basedb.util

This class has methods for autodetecting file formats.

AutoDetectFileFormat() - Constructor for class net.sf.basedb.util.AutoDetectFileFormat

AutoDetectFileFormat.IsImportableFilter - Class in net.sf.basedb.util

Filter implementation that filters a collection of ContextUtil.ContextResult:s by checking each plug-ins ability to import a given file.

AutoDetectingImporter - Interface in net.sf.basedb.core.plugin

This interface should be implemented by an import plugin that supports auto-detection of the file format.

autoFormatter - Variable in class net.sf.basedb.util.excel.XlsxTableWriter

AutoFormatter - Class in net.sf.basedb.util.excel

Excel formatter implementation that automatically selects a format depending on the type/class of the value.

AutoFormatter() - Constructor for class net.sf.basedb.util.excel.AutoFormatter

autoInherit(DbControl, Collection<AnnotationType>, SnapshotManager, boolean) - Method in class net.sf.basedb.core.AnnotationSet

Automatically inherit all annotations of one or more specified annotation types from parent items that are currntly missing from this annotation set

AutoItemExportFormatter - Class in net.sf.basedb.clients.web.formatter

Formatter implementation designed for exporting that generates output with best supported method depending on their type.

AutoItemExportFormatter() - Constructor for class net.sf.basedb.clients.web.formatter.AutoItemExportFormatter

autoJoin() - Method in class net.sf.basedb.core.AbstractQuery

AutoJoiner<Q extends Query,E extends QueryElement> - Interface in net.sf.basedb.core.query

An AutoJoiner is an object that automatically joins other tables in query depending on other query elements.

autoJoiners - Variable in class net.sf.basedb.core.AbstractQuery

autoJoinType - Variable in class net.sf.basedb.core.query.ReporterListExpression

AutoLinkFormatter - Class in net.sf.basedb.clients.web.formatter

Formatter implementation that generates a HTML output trying to link items with best supported method depending on their type.

AutoLinkFormatter() - Constructor for class net.sf.basedb.clients.web.formatter.AutoLinkFormatter

AutoLinkFormatter(boolean, boolean) - Constructor for class net.sf.basedb.clients.web.formatter.AutoLinkFormatter

AutoLinkFormatter(FileViewerUtil) - Constructor for class net.sf.basedb.clients.web.formatter.AutoLinkFormatter

autoLoadChildren - Variable in class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory

autoLogout() - Static method in class net.sf.basedb.core.Session

Cleanup method that sets a logout-time on all sessions that doesn't have a logout time.

autoLogoutSessions - Variable in class net.sf.basedb.core.Application.StartupOptions

autoLogoutSessions(boolean) - Method in class net.sf.basedb.core.Application.StartupOptions

Set to TRUE to automatically set a logout time for all sessions that doesn't have one.

autoPermission - Variable in class net.sf.basedb.core.data.ProjectData

autoReload - Variable in class net.sf.basedb.util.units.UnitCache

autoShare - Variable in class net.sf.basedb.core.data.DirectoryData

autoShow - Variable in class net.sf.basedb.clients.web.taglib.table.Cell

autoUnloadPlugins - Static variable in class net.sf.basedb.core.Application

Allow automatic unload of plug-in JAR files or not.

autoUnloadPlugins() - Static method in class net.sf.basedb.core.Application

If external plug-in JAR files should automatically be unloaded if the are modified.

available() - Method in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream

available() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.WorkbookStream

available() - Method in class net.sf.basedb.util.gtf.GtfInputStream

available() - Method in class net.sf.basedb.util.InputStreamCombiner

available() - Method in class net.sf.basedb.util.InputStreamSplitter

available() - Method in class net.sf.basedb.util.InputStreamTracker

averageMethod - Variable in class net.sf.basedb.clients.web.taglib.table.TableColumn

averageMethod - Variable in class net.sf.basedb.core.data.ExtraValueTypeData

averageMethod - Variable in class net.sf.basedb.core.data.FormulaData

averageMethod - Variable in class net.sf.basedb.core.data.ReporterClonePropertyData

averageMethod - Variable in class net.sf.basedb.core.ExtendedProperty

averageMethod - Variable in enum class net.sf.basedb.core.IntensityTransform

averageMethod - Variable in class net.sf.basedb.util.export.spotdata.JepDynamicField

averageMethod - Variable in class net.sf.basedb.util.export.spotdata.SimpleDynamicField

AverageMethod(int, String) - Constructor for enum class net.sf.basedb.core.Formula.AverageMethod

averageOnReporter - Variable in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

avg - Variable in class net.sf.basedb.core.query.GeometricMeanExpression

avoid(Item, Set<Integer>) - Method in class net.sf.basedb.util.listable.TransformContext

Avoid collected items by removing them from the source set.

avoiding - Variable in class net.sf.basedb.util.listable.TransformContext

B

BACKSLASH - Static variable in class net.sf.basedb.clients.web.util.HTML

BAM - Static variable in class net.sf.basedb.core.DataFileType

The external ID for the file type representing a BAM (Binary Sequence Alignment/Map) file.

barcode - Variable in class net.sf.basedb.core.data.ArraySlideData

barcode - Variable in class net.sf.basedb.core.data.BioPlateData

barcode - Variable in class net.sf.basedb.core.data.PlateData

BARCODE - Static variable in class net.sf.basedb.core.Tag

The ID for the BARCODE tag type.

BARCODE - Static variable in class net.sf.basedb.plugins.batchimport.PropertyIdMethod

Use the barcode for finding items.

barcodeColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.ArraySlideImporter

barcodeColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter

barcodeColumnMapping - Static variable in class net.sf.basedb.plugins.PlateFlatFileImporter

barcodeExists(DbControl, String) - Static method in class net.sf.basedb.core.ArraySlide

Checks if a slide with the given barcode already exists in the database.

barcodeMapper - Variable in class net.sf.basedb.plugins.batchimport.ArraySlideImporter

barcodeMapper - Variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter

barcodeMapper - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter

bas - Variable in class net.sf.basedb.plugins.BaseFileExporterPlugin

bas - Variable in class net.sf.basedb.plugins.BfsExporterPlugin

bas - Variable in class net.sf.basedb.util.jep.ExtraValueFunction

base - Variable in class net.sf.basedb.core.query.LogExpression

base - Variable in class net.sf.basedb.core.query.PowerExpression

Base - Class in net.sf.basedb.clients.web

This class is used to collect some useful methods for the web client into a single place.

Base() - Constructor for class net.sf.basedb.clients.web.Base

BASE_APP_ID - Static variable in class net.sf.basedb.core.data.SchemaVersionData

BASE_VERSION - Static variable in class net.sf.basedb.clients.web.taglib.Page

The version of BASE.

Base1FieldConverter - Class in net.sf.basedb.util.export.spotdata

Exportable field converter that support BASE 1 naming conventions.

Base1FieldConverter(DbControl, BioAssaySet) - Constructor for class net.sf.basedb.util.export.spotdata.Base1FieldConverter

Create a new converter for the given bioassay set.

Base1JobParameterType(char) - Constructor for enum class net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType

Base1PluginExecuter - Class in net.sf.basedb.plugins

This plug-in executes a plug-in from the Base1 system.

Base1PluginExecuter() - Constructor for class net.sf.basedb.plugins.Base1PluginExecuter

Base1PluginExecuter.Base1JobParameterType - Enum Class in net.sf.basedb.plugins

Base1PluginExecuter.JobParameter - Class in net.sf.basedb.plugins

base64_code - Static variable in class net.sf.basedb.util.bcrypt.BCrypt

baseBeginDataPart() - Method in class net.sf.basedb.util.basefile.BaseFileWriter

End the header part of the current section (by writing a single % on a line by itself) and start the data part.

baseBeginSection(String) - Method in class net.sf.basedb.util.basefile.BaseFileWriter

Start a new section in the BASEfile.

baseCompleted - Variable in class net.sf.basedb.core.SimpleAbsoluteProgressReporter

baseEndSection() - Method in class net.sf.basedb.util.basefile.BaseFileWriter

Ends the current section by writing an empty line.

baseEscape(String) - Method in class net.sf.basedb.util.basefile.BaseFileWriter

Escape new line and carrige return characters in the input to the literal string '\n' and '\r' in the output.

BaseException - Exception in net.sf.basedb.core

This is the base class for exceptions in BASE.

BaseException() - Constructor for exception net.sf.basedb.core.BaseException

Create a new BaseException object.

BaseException(String) - Constructor for exception net.sf.basedb.core.BaseException

Create a new BaseException object with the specified message

BaseException(String, Throwable) - Constructor for exception net.sf.basedb.core.BaseException

Create a new BaseException object with the specified message

BaseException(Throwable) - Constructor for exception net.sf.basedb.core.BaseException

Create a new BaseException object acting as a wrapper for another exception that caused the error.

BaseException(SQLException) - Constructor for exception net.sf.basedb.core.BaseException

Create a new BaseException object where the cause is an SQLException.

BASEFILE_MATRIX - Static variable in class net.sf.basedb.core.DataFileType

The external ID for the file type representing a matrix BASEFile.

BASEFILE_SERIAL - Static variable in class net.sf.basedb.core.DataFileType

The external ID for the file type representing a serial BASEFile.

BaseFileExporter - Class in net.sf.basedb.util.export.spotdata

A superclass for exporters that exports spot data to BASEfile format.

BaseFileExporter() - Constructor for class net.sf.basedb.util.export.spotdata.BaseFileExporter

BaseFileExporterPlugin - Class in net.sf.basedb.plugins

Exports bioassay set data as serial or matrix BASEfile:s.

BaseFileExporterPlugin() - Constructor for class net.sf.basedb.plugins.BaseFileExporterPlugin

BaseFileExporterPlugin.ExtendedDynamicField - Class in net.sf.basedb.plugins

BaseFileExporterSupport - Class in net.sf.basedb.plugins.executor

Exporter implementation for the external program executor that exports data to BASEfile format.

BaseFileExporterSupport() - Constructor for class net.sf.basedb.plugins.executor.BaseFileExporterSupport

BaseFileImporter - Class in net.sf.basedb.util.importer.spotdata

Imports spot data from a serial or matrix BASEfile.

BaseFileImporter() - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileImporter

Create a new importer object.

BaseFileImporter.RawDataProxy - Class in net.sf.basedb.util.importer.spotdata

BaseFileImporter.ReporterProxy - Class in net.sf.basedb.util.importer.spotdata

BaseFileImporterSupport - Class in net.sf.basedb.plugins.executor

Importer implementation for the external program executor that imports data from BASEfile format.

BaseFileImporterSupport() - Constructor for class net.sf.basedb.plugins.executor.BaseFileImporterSupport

BaseFileInfo - Class in net.sf.basedb.util.importer.spotdata

Collects information about a BASEfile as it gets parsed by a BaseFileImporter.

BaseFileInfo(FileWrapper) - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileInfo

The source file which should be a BASEfile.

BaseFileInfo.ChildBioAssay - Class in net.sf.basedb.util.importer.spotdata

Keeps information about a new child bioassay from the 'assays' section or 'spot' sections.

BaseFileInfo.SpotSectionInfo - Class in net.sf.basedb.util.importer.spotdata

Keeps information about headers and more in a 'spot' section.

BaseFileParser - Class in net.sf.basedb.util.basefile

Parser for serial and matrix BASEfile:s.

BaseFileParser() - Constructor for class net.sf.basedb.util.basefile.BaseFileParser

Creates a new parser object.

BaseFileSectionParser - Interface in net.sf.basedb.util.basefile

A section parser is responsible for parsing and collecting data that is found in a section in a serial or matrix BASEfile.

BaseFileWrapper - Class in net.sf.basedb.util.importer

File wrapper implementation for files that are located on the BASE file system.

BaseFileWrapper(File) - Constructor for class net.sf.basedb.util.importer.BaseFileWrapper

BaseFileWriter - Class in net.sf.basedb.util.basefile

Wraps a writer stream and provides methods for easier creation of BASEfiles.

BaseFileWriter(Writer) - Constructor for class net.sf.basedb.util.basefile.BaseFileWriter

Create a new BASEfile writer that is writing it's output to the given writer.

BaseInputStreamLocator - Class in net.sf.basedb.util.bfs

Input stream locator implementation that works with files within a given directory in the BASE file system.

BaseInputStreamLocator(DbControl, Directory) - Constructor for class net.sf.basedb.util.bfs.BaseInputStreamLocator

Create a new input stream locator.

basePrintData(Object...) - Method in class net.sf.basedb.util.basefile.BaseFileWriter

Print a data line to the BASEfile.

basePrintHeader(String, Object) - Method in class net.sf.basedb.util.basefile.BaseFileWriter

Prints a header in the BASEfile.

baseStyle - Variable in class net.sf.basedb.util.excel.CellStyleCreator

baseWriteBom() - Method in class net.sf.basedb.util.basefile.BaseFileWriter

Write the beginning-of-file marker (BASEfile) to the output.

basic - Static variable in class net.sf.basedb.core.Item.DefinedPermissions

BASIC_FILTER - Static variable in class net.sf.basedb.core.QueryRuntimeFilterFactory

BasicBatcher<D extends BatchableData> - Class in net.sf.basedb.core

This is an abstract class for batching functionallity.

BasicBatcher(Session, Class<D>, String) - Constructor for class net.sf.basedb.core.BasicBatcher

Constructor that initiate everything.

BasicChildItem - Class in net.sf.basedb.core

An abstract base class for all items which are child items to a BasicItem parent item.

BasicChildItem(BasicData) - Constructor for class net.sf.basedb.core.BasicChildItem

BasicData - Class in net.sf.basedb.core.data

This is the root superclass of all data classes.

BasicData() - Constructor for class net.sf.basedb.core.data.BasicData

BasicData2ItemPropertyPath(Item, Type) - Constructor for class net.sf.basedb.core.Metadata.BasicData2ItemPropertyPath

BasicFilter() - Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.BasicFilter

BasicItem - Class in net.sf.basedb.core

This is the root superclass of all item classes.

BasicItem(BasicData) - Constructor for class net.sf.basedb.core.BasicItem

Create a new instance.

BasicItem2DataPropertyPath(Class<C>, Type) - Constructor for class net.sf.basedb.core.Metadata.BasicItem2DataPropertyPath

BasicItemFilter - Class in net.sf.basedb.util.overview.filter

A filter implementation that matches against the item that is attached to nodes.

BasicItemFilter(BasicItem) - Constructor for class net.sf.basedb.util.overview.filter.BasicItemFilter

Create a filter that finds nodes that has the given item attached to it.

BasicItemNodeLoader<I extends BasicItem> - Class in net.sf.basedb.util.overview.loader

Abstract class that is useful for all node loaders that works with BasicItem:s.

BasicItemNodeLoader(Object, boolean, NodeNameGenerator<I>) - Constructor for class net.sf.basedb.util.overview.loader.BasicItemNodeLoader

Create a new node loader.

BasicItemNodeLoaderFactory - Class in net.sf.basedb.util.overview.loader

Node loader factory implementation for BasicItem node loaders.

BasicItemNodeLoaderFactory() - Constructor for class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory

Creates a new factory.

BasicItemNodeValidatorFactory - Class in net.sf.basedb.util.overview.validator

Node validator factory implementation for BasicItem node validators.

BasicItemNodeValidatorFactory() - Constructor for class net.sf.basedb.util.overview.validator.BasicItemNodeValidatorFactory

Creates a new factory.

BasicItemToIdTransformer - Class in net.sf.basedb.util.collections

Collection transformer implementation that extracts the ID from BasicItem:s.

BasicItemToIdTransformer() - Constructor for class net.sf.basedb.util.collections.BasicItemToIdTransformer

BasicNodeValidator<I> - Class in net.sf.basedb.util.overview.validator

A simple node validation implementation that takes care of missing and denied access to items.

BasicNodeValidator(Validator, Validator) - Constructor for class net.sf.basedb.util.overview.validator.BasicNodeValidator

Creates a new validator.

BatchableData - Interface in net.sf.basedb.core.data

This is a tagging interface only.

BatchAndMapHolder(RawDataBatcher, RawDataType, FlatFileParser) - Constructor for class net.sf.basedb.plugins.IlluminaRawDataImporter.BatchAndMapHolder

batchCount - Variable in class net.sf.basedb.core.LogControl

batchDate - Variable in class net.sf.basedb.core.AnnotationBatcher

batchedExternalIds - Variable in class net.sf.basedb.core.ReporterBatcher

A set containing all batched but not yet flushed external reporter id:s.

BatchedPropertyInfo - Class in net.sf.basedb.core

Holds information about a batchable property.

BatchedPropertyInfo(String, int) - Constructor for class net.sf.basedb.core.BatchedPropertyInfo

Create a new extended property.

batcher - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

batcher - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter.BatchAndMapHolder

batcher - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter

batcher - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

batcher - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

batcher - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

Batcher - Interface in net.sf.basedb.core

The basic interface which all batchers must implement.

batchers - Variable in class net.sf.basedb.core.DbControl

A list of batchers that will be closed when DbControl is closed and will be flushed when commit is called.

batchIndex - Variable in class net.sf.basedb.core.data.ArraySlideData

batchQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

batchSize - Variable in class net.sf.basedb.core.AbstractBatcher

SQL command batch size.

batchSize - Variable in class net.sf.basedb.core.LogControl

BatchUtil - Class in net.sf.basedb.core

Utility class for batching information.

BatchUtil() - Constructor for class net.sf.basedb.core.BatchUtil

BCrypt - Class in net.sf.basedb.util.bcrypt

BCrypt implements OpenBSD-style Blowfish password hashing using the scheme described in "A Future-Adaptable Password Scheme" by Niels Provos and David Mazieres.

BCrypt() - Constructor for class net.sf.basedb.util.bcrypt.BCrypt

BCRYPT_SALT_LEN - Static variable in class net.sf.basedb.util.bcrypt.BCrypt

bean - Variable in class net.sf.basedb.util.extensions.debug.BeanActionFactory

BeanActionFactory - Class in net.sf.basedb.util.extensions.debug

Generic action factory class that can generate instances of actions if there exists a bean-like implementation of the action class.

BeanActionFactory() - Constructor for class net.sf.basedb.util.extensions.debug.BeanActionFactory

Creates a new proxy factory.

beanClassName - Variable in class net.sf.basedb.util.extensions.debug.BeanActionFactory

before - Variable in class net.sf.basedb.core.DbControl.SaveIf

BEFORE_DISABLE - Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl

This event is sent before an extension or extension point is disabled by ExtensionsControl.enableExtensionPoint(String, boolean), ExtensionsControl.enableExtension(String, boolean), or ExtensionsControl.enableAllInFile(String, boolean).

BEFORE_UNREGISTRATION - Static variable in class net.sf.basedb.util.extensions.events.EventType

This event is sent before an extension point or extension is unregistered.

BEFORE_UPDATE - Static variable in class net.sf.basedb.util.extensions.events.EventType

This event is sent during an update of an existing extension point or extension.

beforeTransactionCompletion(Transaction) - Method in class net.sf.basedb.core.log.LoggingInterceptor

Flush remaining changes in the log control.

begin(DbControl) - Method in class net.sf.basedb.clients.web.plugins.SimpleExport

begin(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin

Called just before the export starts.

begin(DbControl) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin

begin(DbControl) - Method in class net.sf.basedb.plugins.BfsExporterPlugin

begin(DbControl) - Method in class net.sf.basedb.plugins.GalExporter

begin(DbControl) - Method in class net.sf.basedb.plugins.HelpExporter

begin(DbControl) - Method in class net.sf.basedb.plugins.PackedFileExporter

begin(DbControl) - Method in class net.sf.basedb.plugins.PlateMappingExporter

begin(DbControl) - Method in class net.sf.basedb.plugins.PluginConfigurationExporter

begin(ExtensionsManager, int) - Method in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor

begin(ExtensionsManager, int) - Method in class net.sf.basedb.clients.web.extensions.UninstalledFileProcessor

begin(ExtensionsManager, int) - Method in interface net.sf.basedb.util.extensions.manager.ExtensionsFileProcessor

Called by the extensions manager before the processing starts.

begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor

begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor

begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor

begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.IgnoreFileProcessor

begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.MarkAsProcessedProcessor

begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor

begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor

begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor

begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor

begin(FlatFileParser) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

Called just before parsing of the file begins.

begin(FlatFileParser) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter

Setup error handling and pre-load some of the configuration options.

begin(FlatFileParser) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Setup error handling and pre-load some of the configuration options.

begin(FlatFileParser) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

Setup error handling and pre-load some of the configuration options.

begin(FlatFileParser) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter

begin(FlatFileParser) - Method in class net.sf.basedb.plugins.PlateFlatFileImporter

Create a DbControl and a RawDataBatcher.

begin(FlatFileParser) - Method in class net.sf.basedb.plugins.PlateMappingImporter

Save reference to parser.

begin(FlatFileParser) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter

Create a DbControl and a FeatureBatcher.

begin(FlatFileParser) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter

Prepare for importing the next file.

begin(FlatFileParser) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter

Create a DbControl and a ReporterBatcher.

begin(FlatFileParser) - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

Create a DbControl and a FeatureBatcher.

beginData() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

Called by the parser after the headers have been parsed but before the first data line is parsed.

beginData() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter

Setup column mapping.

beginData() - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Setup column mapping.

beginData() - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

Setup column mapping.

beginData() - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter

Check column headers and map them to raw bioassays.

beginData() - Method in class net.sf.basedb.plugins.PlateFlatFileImporter

Initialise column Mapper:s.

beginData() - Method in class net.sf.basedb.plugins.PlateMappingImporter

Create a DbControl and a new PlateMapping.

beginData() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter

Initialise column Mapper:s.

beginData() - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter

Initialise column Mapper:s.

beginData() - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

Initialise column Mapper:s.

beginDocument() - Method in interface net.sf.basedb.clients.web.plugins.ExportTemplate

Start writing the document.

beginDocument() - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate

Do nothing.

beginDocument() - Method in class net.sf.basedb.clients.web.plugins.XlsxTemplate

Reset row and column to 0.

beginDocument() - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate

Write XML start (<?

beginExport() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

Make preparations for the export.

beginExport() - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter

Prepare the export by adding all experimental factors as assay fields if no fields have been specified.

beginExport() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter

Validates that all required properties has been set and initialises other things that are needed.

beginExport() - Method in class net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter

Prepare the export by pre-loading some information and configure the queries that we are going to use.

beginExport() - Method in class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter

Prepare the export by pre-loading some information and configure the queries that we are going to use.

beginItem(int) - Method in interface net.sf.basedb.clients.web.plugins.ExportTemplate

Start writing a new item.

beginItem(int) - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate

Reset column number.

beginItem(int) - Method in class net.sf.basedb.clients.web.plugins.XlsxTemplate

Reset column number and create a new row.

beginItem(int) - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate

Begin a new item element.

beginSection(BaseFileParser, FlatFileParser, List<String>) - Method in class net.sf.basedb.util.importer.spotdata.GenericIntensityParser

beginSection(BaseFileParser, FlatFileParser, List<String>) - Method in class net.sf.basedb.util.importer.spotdata.MAParser

beginSection(BaseFileParser, FlatFileParser, List<String>) - Method in interface net.sf.basedb.util.importer.spotdata.SpotIntensityParser

Prepare for parsing the data section.

beginTransaction() - Method in class net.sf.basedb.core.hibernate.SessionWrapper

beginTransaction() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

belongsTo(AnnotationSet) - Method in class net.sf.basedb.core.Annotation

Check if this annotation belongs to the primaray annotations for a specified annotation set.

between(Expression, Expression, Expression) - Static method in class net.sf.basedb.core.query.Restrictions

Compare if one expression falls between two other expressions: new expression = low <= e AND e < high.

BETWEEN - Enum constant in enum class net.sf.basedb.core.Operator

betweenInclusive(Expression, Expression, Expression) - Static method in class net.sf.basedb.core.query.Restrictions

Compare if one expression falls between two other expressions (inclusive): new expression = low <= e AND e <= high.

BetweenRestriction - Class in net.sf.basedb.core.query

Compare if one expression falls between to other expressions: e BETWEEN low AND high.

BetweenRestriction(Expression, Expression, Expression, boolean) - Constructor for class net.sf.basedb.core.query.BetweenRestriction

bf_crypt_ciphertext - Static variable in class net.sf.basedb.util.bcrypt.BCrypt

BFS_METADATA - Static variable in class net.sf.basedb.core.DataFileType

The external ID for the file type representing a BFS metadata file.

BfsExporter - Class in net.sf.basedb.util.export.spotdata

Base class for exporting spotdata to BFS format.

BfsExporter() - Constructor for class net.sf.basedb.util.export.spotdata.BfsExporter

BfsExporterPlugin - Class in net.sf.basedb.plugins

Exports bioassay set data to BFS format.

BfsExporterPlugin() - Constructor for class net.sf.basedb.plugins.BfsExporterPlugin

BfsExporterPlugin.ExtendedExportableField - Class in net.sf.basedb.plugins

BfsExporterSupport - Class in net.sf.basedb.plugins.executor

Exporter implementation for the external program executor that exports data to BFS format.

BfsExporterSupport() - Constructor for class net.sf.basedb.plugins.executor.BfsExporterSupport

BfsImporter - Class in net.sf.basedb.util.importer.spotdata

Imports spot data from a serial or matrix BFS.

BfsImporter() - Constructor for class net.sf.basedb.util.importer.spotdata.BfsImporter

Create a new importer object.

BfsImporter.ProgressEventHandler - Class in net.sf.basedb.util.importer.spotdata

BfsImporterSupport - Class in net.sf.basedb.plugins.executor

Importer implementation for the external program executor that imports data from BFS format.

BfsImporterSupport() - Constructor for class net.sf.basedb.plugins.executor.BfsImporterSupport

BfsParser - Interface in net.sf.basedb.util.bfs

Interface that it is recommended that all BFS parsers should implement.

bfsPrintComment(String) - Method in class net.sf.basedb.util.bfs.MetadataWriter

Prints one or more comment lines to the metadata file.

bfsPrintData(int, Object...) - Method in class net.sf.basedb.util.bfs.AnnotationWriter

Print a data line.

bfsPrintData(Object...) - Method in class net.sf.basedb.util.bfs.DataWriter

Print a data line.

bfsPrintEmptyLine(int) - Method in class net.sf.basedb.util.bfs.MetadataWriter

Print one or more empty lines to the metadata file.

bfsPrintHeaders(String...) - Method in class net.sf.basedb.util.bfs.AnnotationWriter

Print the header line.

bfsPrintSection(String, boolean, boolean) - Method in class net.sf.basedb.util.bfs.MetadataWriter

Start a new section.

bfsPrintValue(String, String...) - Method in class net.sf.basedb.util.bfs.MetadataWriter

Prints a section entry.

bfsPrintValue(String, Formatter<T>, T...) - Method in class net.sf.basedb.util.bfs.MetadataWriter

Prints a section entry.

bfsPrintValue(String, T...) - Method in class net.sf.basedb.util.bfs.MetadataWriter

Prints a section entry.

BINARY_ESCAPE - Variable in class net.sf.basedb.core.migrate.postgres.PostgresResultWriterFactory

bins - Variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramSeries

bioassay - Variable in class net.sf.basedb.core.data.ArraySlideData

bioassay - Variable in class net.sf.basedb.core.data.BioMaterialEventData

bioAssay - Variable in class net.sf.basedb.core.data.RawBioAssayData

BioAssay - Class in net.sf.basedb.core

Represents the current intensities of raw data after some transformation has been applied to it.

BioAssay(BioAssayData) - Constructor for class net.sf.basedb.core.BioAssay

Creates a new bioassay item from the given data.

BIOASSAY - Enum constant in enum class net.sf.basedb.core.BioMaterialEvent.Type

An event of this type created a physical bioassay.

BIOASSAY - Enum constant in enum class net.sf.basedb.core.Item

The item is a BioAssay

bioAssayColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

BioAssayData - Class in net.sf.basedb.core.data

This class holds information about a bioassay.

BioAssayData() - Constructor for class net.sf.basedb.core.data.BioAssayData

BioAssayExperimentalFactorLoader - Class in net.sf.basedb.clients.web.plugins

Data loader that gets annotation values for a bioassay including those that are present on the parent raw bioassay(s) without being directly inherited by the bioassay.

BioAssayExperimentalFactorLoader() - Constructor for class net.sf.basedb.clients.web.plugins.BioAssayExperimentalFactorLoader

BioAssayExperimentalFactorLoader(SnapshotManager) - Constructor for class net.sf.basedb.clients.web.plugins.BioAssayExperimentalFactorLoader

Creates an experimental factor loader that uses a specific snapshot manager for loading the annotation values.

bioAssayId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba

bioAssayMapper - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

bioAssays - Variable in class net.sf.basedb.clients.web.ExperimentExplorer

Maps a bioassays cube column number to it's id for fast loading by the ExperimentExplorer.getBioAssay(DbControl, short) method.

bioAssays - Variable in class net.sf.basedb.core.data.BioAssaySetData

bioAssays - Variable in class net.sf.basedb.core.data.RawBioAssayData

bioAssays - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter

bioAssays - Variable in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

bioAssays - Variable in class net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter

bioAssays - Variable in class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter

bioAssaySet - Variable in class net.sf.basedb.clients.web.ExperimentExplorer

The bioassay set we are exploring.

bioAssaySet - Variable in class net.sf.basedb.core.data.BioAssayData

bioAssaySet - Variable in class net.sf.basedb.core.data.ExtraValueData

bioAssaySet - Variable in class net.sf.basedb.core.DynamicPositionQuery

bioAssaySet - Variable in class net.sf.basedb.core.DynamicSpotQuery

bioAssaySet - Variable in class net.sf.basedb.core.FilterBatcher

The bioassayset this batcher inserts data for.

bioAssaySet - Variable in class net.sf.basedb.core.SpotBatcher

The bioassayset this batcher inserts data for.

BioAssaySet - Class in net.sf.basedb.core

A bioassayset represents the current intensities of the raw data after some Transformation has been applied to it.

BioAssaySet(BioAssaySetData) - Constructor for class net.sf.basedb.core.BioAssaySet

Creates a new experiment item from the given data.

BIOASSAYSET - Enum constant in enum class net.sf.basedb.core.Item

The item is a BioAssaySet

BioAssaySetData - Class in net.sf.basedb.core.data

This class holds information about a bioassayset.

BioAssaySetData() - Constructor for class net.sf.basedb.core.data.BioAssaySetData

BioAssaySetFilterUtil - Class in net.sf.basedb.util

This is a utility class for plugins that filters bioassay set data.

BioAssaySetFilterUtil() - Constructor for class net.sf.basedb.util.BioAssaySetFilterUtil

bioAssaySets - Variable in class net.sf.basedb.core.data.ExperimentData

BioAssaySetUtil - Class in net.sf.basedb.util

This is a utility class for BioAssaySet.

BioAssaySetUtil() - Constructor for class net.sf.basedb.util.BioAssaySetUtil

bioAssaySpots - Variable in class net.sf.basedb.core.BioAssaySet

Stores the result of BioAssaySet.getSpotCount(int).

bioMaterial - Variable in class net.sf.basedb.core.data.BioMaterialEventData

bioMaterial - Variable in class net.sf.basedb.core.data.BioMaterialEventSourceData

bioMaterial - Variable in class net.sf.basedb.core.data.BioWellData

bioMaterial - Variable in class net.sf.basedb.core.MeasuredBioMaterial.RemainingQuantityAction

BioMaterial - Class in net.sf.basedb.core

This is the base class for for the three types of biomaterials: BioSource, Sample and Extract.

BioMaterial(BioMaterialData) - Constructor for class net.sf.basedb.core.BioMaterial

BioMaterialData - Class in net.sf.basedb.core.data

This class is the root class for biomaterials.

BioMaterialData() - Constructor for class net.sf.basedb.core.data.BioMaterialData

BioMaterialEvent - Class in net.sf.basedb.core

This class represents an event in the life of a MeasuredBioMaterial.

BioMaterialEvent(BioMaterialEventData) - Constructor for class net.sf.basedb.core.BioMaterialEvent

BIOMATERIALEVENT - Enum constant in enum class net.sf.basedb.core.Item

The item is a BioMaterialEvent.

BioMaterialEvent.Type - Enum Class in net.sf.basedb.core

The type of the event.

BioMaterialEventData - Class in net.sf.basedb.core.data

This class is used to register events for measured biomaterials.

BioMaterialEventData() - Constructor for class net.sf.basedb.core.data.BioMaterialEventData

BioMaterialEventLogger - Class in net.sf.basedb.core.log.db

Logger for biomaterial events that logs UPDATE:s to CREATION and HYBRIDIZATION events as updates to their parent biomaterial/hybridization.

BioMaterialEventLogger(DbLogManagerFactory) - Constructor for class net.sf.basedb.core.log.db.BioMaterialEventLogger

Creates a new biomaterial event logger.

bioMaterialEvents - Variable in class net.sf.basedb.core.data.BioPlateEventParticipantData

BioMaterialEventSource - Class in net.sf.basedb.core

Class for holding information about a parent biomaterial that was used in an event that created a child biomaterial or a physical bioassay.

BioMaterialEventSource(DbControl, BioMaterialEventSourceData) - Constructor for class net.sf.basedb.core.BioMaterialEventSource

BioMaterialEventSource.BioMaterialEventSourceTransformer - Class in net.sf.basedb.core

BioMaterialEventSourceData - Class in net.sf.basedb.core.data

Data class for holding information about a parent biomaterial that was used in an event that created a child biomaterial or a physical bioassay.

BioMaterialEventSourceData() - Constructor for class net.sf.basedb.core.data.BioMaterialEventSourceData

BioMaterialEventSourceFormatter - Class in net.sf.basedb.clients.web.plugins

Formatter to handle BioMaterialEventSource items.

BioMaterialEventSourceFormatter() - Constructor for class net.sf.basedb.clients.web.plugins.BioMaterialEventSourceFormatter

Create a new formatter.

BioMaterialEventSourceFormatter(String) - Constructor for class net.sf.basedb.clients.web.plugins.BioMaterialEventSourceFormatter

Create a new formatter.

BioMaterialEventSourceTransformer() - Constructor for class net.sf.basedb.core.BioMaterialEventSource.BioMaterialEventSourceTransformer

bioMaterialType - Variable in class net.sf.basedb.core.data.BioPlateTypeData

bioPlate - Variable in class net.sf.basedb.core.data.BioPlateEventParticipantData

bioPlate - Variable in class net.sf.basedb.core.data.BioWellData

BioPlate - Class in net.sf.basedb.core

This class is represents physical bio-plates.

BioPlate(BioPlateData) - Constructor for class net.sf.basedb.core.BioPlate

BIOPLATE - Enum constant in enum class net.sf.basedb.core.Item

The item is a BioPlate

bioPlateColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.SampleImporter

Column mapping parameter for the bioplate

BioPlateData - Class in net.sf.basedb.core.data

This class holds information about a bioplate

BioPlateData() - Constructor for class net.sf.basedb.core.data.BioPlateData

BioPlateEvent - Class in net.sf.basedb.core

A bioplate event represents something that happened simultaneously to the biomaterial on one or more bioplates.

BioPlateEvent(BioPlateEventData) - Constructor for class net.sf.basedb.core.BioPlateEvent

BIOPLATEEVENT - Enum constant in enum class net.sf.basedb.core.Item

The item is a BioPlateEvent

BioPlateEventData - Class in net.sf.basedb.core.data

This class holds information about a bioplate event.

BioPlateEventData() - Constructor for class net.sf.basedb.core.data.BioPlateEventData

BioPlateEventLoader - Class in net.sf.basedb.util.overview.loader

Node loader implementation for bioplate events.

BioPlateEventLoader() - Constructor for class net.sf.basedb.util.overview.loader.BioPlateEventLoader

bioPlateEventParticipant - Variable in class net.sf.basedb.core.data.BioMaterialEventData

bioPlateEventParticipant - Variable in class net.sf.basedb.core.MeasuredBioMaterial

bioPlateEventParticipant - Variable in class net.sf.basedb.core.PhysicalBioAssay

BioPlateEventParticipant - Class in net.sf.basedb.core

Holds information about a bioplate that is participating in a bioplate event.

BioPlateEventParticipant(BioPlateEventParticipantData) - Constructor for class net.sf.basedb.core.BioPlateEventParticipant

BIOPLATEEVENTPARTICIPANT - Enum constant in enum class net.sf.basedb.core.Item

The item is a BioPlateEventParticipant

BioPlateEventParticipantData - Class in net.sf.basedb.core.data

Registers a plate as a participant in a bioplate event.

BioPlateEventParticipantData() - Constructor for class net.sf.basedb.core.data.BioPlateEventParticipantData

BioPlateEventType - Class in net.sf.basedb.core

The type of a bioplate event defines what happened in the event.

BioPlateEventType(BioPlateEventTypeData) - Constructor for class net.sf.basedb.core.BioPlateEventType

BIOPLATEEVENTTYPE - Enum constant in enum class net.sf.basedb.core.Item

The item is a BioPlateEventType

BioPlateEventTypeData - Class in net.sf.basedb.core.data

Each bioplate event must have a type that defines what happened.

BioPlateEventTypeData() - Constructor for class net.sf.basedb.core.data.BioPlateEventTypeData

BioPlateImporter - Class in net.sf.basedb.plugins.batchimport

Plug-in for importing bioplate items in a batch.

BioPlateImporter() - Constructor for class net.sf.basedb.plugins.batchimport.BioPlateImporter

BioPlateLoader - Class in net.sf.basedb.util.overview.loader

Node loader implementation for bioplates.

BioPlateLoader() - Constructor for class net.sf.basedb.util.overview.loader.BioPlateLoader

bioPlateMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter

bioPlateMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter

BioPlateNameGenerator - Class in net.sf.basedb.util.overview.node

Name generator implementation for BioPlate items.

BioPlateNameGenerator(String, String) - Constructor for class net.sf.basedb.util.overview.node.BioPlateNameGenerator

Create a new name generator.

bioPlateQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

bioPlates - Variable in class net.sf.basedb.core.data.BioPlateTypeData

bioPlateType - Variable in class net.sf.basedb.core.data.BioPlateData

BioPlateType - Class in net.sf.basedb.core

This class represents the type of a bio-plate.

BioPlateType(BioPlateTypeData) - Constructor for class net.sf.basedb.core.BioPlateType

BIOPLATETYPE - Enum constant in enum class net.sf.basedb.core.Item

The item is a BioPlateType.

bioPlateTypeColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter

BioPlateTypeData - Class in net.sf.basedb.core.data

This class holds information about a biomaterial plate type.

BioPlateTypeData() - Constructor for class net.sf.basedb.core.data.BioPlateTypeData

bioPlateTypeMapper - Variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter

bioPlateTypeQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

BioPlateValidator - Class in net.sf.basedb.util.overview.validator

Validator implementation for bioplates.

BioPlateValidator() - Constructor for class net.sf.basedb.util.overview.validator.BioPlateValidator

BioSource - Class in net.sf.basedb.core

This class represent biosource items.

BioSource(BioSourceData) - Constructor for class net.sf.basedb.core.BioSource

BIOSOURCE - Enum constant in enum class net.sf.basedb.core.Item

The item is a BioSource.

BioSourceData - Class in net.sf.basedb.core.data

This represents a biosoruce which is the starting point of all biomaterials.

BioSourceData() - Constructor for class net.sf.basedb.core.data.BioSourceData

BioSourceImporter - Class in net.sf.basedb.plugins.batchimport

Plug-in for importing biosource items in a batch.

BioSourceImporter() - Constructor for class net.sf.basedb.plugins.batchimport.BioSourceImporter

BioSourceLoader - Class in net.sf.basedb.util.overview.loader

Node loader implementation for biosources.

BioSourceLoader() - Constructor for class net.sf.basedb.util.overview.loader.BioSourceLoader

bioSourceQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

BioSourceToSampleTransformer - Class in net.sf.basedb.util.listable

Source item transformer that transform biosource items to their child samples.

BioSourceToSampleTransformer() - Constructor for class net.sf.basedb.util.listable.BioSourceToSampleTransformer

BioSourceValidator - Class in net.sf.basedb.util.overview.validator

Validator implementation for biosources.

BioSourceValidator() - Constructor for class net.sf.basedb.util.overview.validator.BioSourceValidator

bioWell - Variable in class net.sf.basedb.core.data.MeasuredBioMaterialData

BioWell - Class in net.sf.basedb.core

A biowell is located on a BioPlate and contains a MeasuredBioMaterial.

BioWell(BioWellData) - Constructor for class net.sf.basedb.core.BioWell

BIOWELL - Enum constant in enum class net.sf.basedb.core.Item

The item is a BioWell

BioWell.LockMode - Enum Class in net.sf.basedb.core

The lock mode for a well is determined by the plate's bio plate type.

bioWellColColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.SampleImporter

Column mapping parameter for the biowell's column

bioWellColMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter

bioWellColMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter

BioWellData - Class in net.sf.basedb.core.data

This class holds information about a bio well on a bio plate.

BioWellData() - Constructor for class net.sf.basedb.core.data.BioWellData

BioWellLoader - Class in net.sf.basedb.util.overview.loader

Node loader implementation that load biomaterial on a bioplate.

BioWellLoader() - Constructor for class net.sf.basedb.util.overview.loader.BioWellLoader

BioWellNameGenerator - Class in net.sf.basedb.util.overview.node

Name generator implementation for biomaterial items that are located on a biowell.

BioWellNameGenerator() - Constructor for class net.sf.basedb.util.overview.node.BioWellNameGenerator

Create a new biowell name generator.

bioWellRowColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.SampleImporter

Column mapping parameter for the biowell's row

bioWellRowMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter

bioWellRowMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter

bioWells - Variable in class net.sf.basedb.core.data.BioPlateData

BlankValue() - Constructor for class net.sf.basedb.util.excel.ExcelValue.BlankValue

block - Variable in class net.sf.basedb.core.BlockInfo

The block number.

block - Variable in class net.sf.basedb.core.data.RawData

block - Variable in class net.sf.basedb.core.FeatureCoordinate

block - Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData

block - Variable in class net.sf.basedb.plugins.MedianRatioNormalization.SpotData

block - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock

BLOCK - Enum constant in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section

blockColumnMapping - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

blockColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

blockGroupParameter - Static variable in class net.sf.basedb.plugins.LowessNormalization

blockGroupParameter - Static variable in class net.sf.basedb.plugins.MedianRatioNormalization

Used with 2-channel data only

blockGroupSize - Variable in class net.sf.basedb.plugins.LowessNormalization.CallableWorker

BlockInfo - Class in net.sf.basedb.core

A BlockInfo object is used to represent the uniqe identifiers of an ArrayDesignBlock.

BlockInfo(int, int) - Constructor for class net.sf.basedb.core.BlockInfo

Create a new block info using the meta coordinates.

BlockInfo(int, int, int) - Constructor for class net.sf.basedb.core.BlockInfo

Create a new block info using meta coordinates.

blockMapper - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

blockMapper - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

blockNumber - Variable in class net.sf.basedb.core.data.ArrayDesignBlockData

blockNumber - Variable in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section

blocks - Variable in class net.sf.basedb.core.ArrayDesign

blocks - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter

blocks - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

blockSizeX - Variable in class net.sf.basedb.core.data.ArrayDesignBlockData

blockSizeX - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock

blockSizeY - Variable in class net.sf.basedb.core.data.ArrayDesignBlockData

blockSizeY - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock

BLOWFISH_NUM_ROUNDS - Static variable in class net.sf.basedb.util.bcrypt.BCrypt

Body - Class in net.sf.basedb.clients.web.taglib

This tag defines the body section of a page.

Body() - Constructor for class net.sf.basedb.clients.web.taglib.Body

BOF_EVENT - Static variable in class net.sf.basedb.util.bfs.MetadataParser

Event type that is issued when the beginning-of-file marker is found.

BOF_MARKER - Static variable in class net.sf.basedb.util.bfs.MetadataWriter

bofMarker - Variable in class net.sf.basedb.util.parser.FlatFileParser

The regular expression for matching the beginning-of-file marker

bofType - Variable in class net.sf.basedb.util.parser.FlatFileParser

The value that was captured by the bofMarker pattern.

bool(boolean) - Static method in class net.sf.basedb.core.query.Expressions

Create a constant expression from a boolean.

bool(Restriction) - Static method in class net.sf.basedb.core.query.Expressions

Create a boolean expression view of a restriction.

BOOLEAN - Enum constant in enum class net.sf.basedb.core.Type

Boolean type.

BOOLEAN - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper

BOOLEAN_FORMAT - Static variable in class net.sf.basedb.clients.web.plugins.SimpleExport

BooleanExpression - Class in net.sf.basedb.core.query

A constant boolean expression.

BooleanExpression(boolean) - Constructor for class net.sf.basedb.core.query.BooleanExpression

BooleanExpression(Restriction) - Constructor for class net.sf.basedb.core.query.BooleanExpression

BooleanFormatter - Class in net.sf.basedb.util.formatter

Formats a boolean value.

BooleanFormatter(BooleanFormatter.Type) - Constructor for class net.sf.basedb.util.formatter.BooleanFormatter

Create a new boolean formatter.

BooleanFormatter.Type - Enum Class in net.sf.basedb.util.formatter

Enum for holding the various types of boolean output.

BooleanParameterType - Class in net.sf.basedb.core

This class represent a parameter type that is a boolean.

BooleanParameterType() - Constructor for class net.sf.basedb.core.BooleanParameterType

Create a new boolean parameter type, allowing null values.

BooleanParameterType(Boolean, boolean) - Constructor for class net.sf.basedb.core.BooleanParameterType

Create a new boolean parameter type.

BooleanParameterType(Boolean, boolean, int, Enumeration<Boolean, String>) - Constructor for class net.sf.basedb.core.BooleanParameterType

BooleanParameterValueData - Class in net.sf.basedb.core.data

Boolean parameter value.

BooleanParameterValueData() - Constructor for class net.sf.basedb.core.data.BooleanParameterValueData

BooleanParameterValueData(Boolean...) - Constructor for class net.sf.basedb.core.data.BooleanParameterValueData

BooleanValue(boolean) - Constructor for class net.sf.basedb.util.excel.ExcelValue.BooleanValue

BooleanWriter - Class in net.sf.basedb.core.migrate

Database-independent writer implementation that writes boolean values from a result set.

BooleanWriter(ResultSet, int, Writer, char[]) - Constructor for class net.sf.basedb.core.migrate.BooleanWriter

BOTTOM - Static variable in class net.sf.basedb.clients.web.taglib.tab.TabControl

Tabs are at the bottom of the tab control.

boundary - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload

The multipart/formdata boundary

breakCircularReferences(Set<ItemProxy>) - Method in class net.sf.basedb.core.BasicItem

Break references to items that may lead to circular references.

breakCircularReferences(Set<ItemProxy>) - Method in class net.sf.basedb.core.DerivedBioAssay

Any parent bioassays found among the given items are removed from this item.

breakCircularReferences(Set<ItemProxy>) - Method in class net.sf.basedb.core.MeasuredBioMaterial

Any parent items found among the given items are removed from the creation event of this item.

breakCircularReferences(Set<ItemProxy>) - Method in class net.sf.basedb.core.User

If the home directory is found among the items, set it to null.

breakCircularReferences(SessionControl, Set<Identifiable>) - Static method in class net.sf.basedb.core.Trashcan

buffer - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream

buffer - Variable in class net.sf.basedb.util.gtf.GtfInputStream

BUFFER_SIZE - Static variable in class net.sf.basedb.util.FileUtil

build - Variable in class net.sf.basedb.core.data.SchemaVersionData

build - Static variable in class net.sf.basedb.core.Version

buildDelete(String, Dialect) - Static method in class net.sf.basedb.core.BatchUtil

Build delete SQL string and put it in the SQL map.

buildDocument() - Method in class net.sf.basedb.core.Presets

Convert the presets to a XML document.

buildDom(Element) - Method in class net.sf.basedb.core.Presets.Preset

Add XML elements to the parent element for this preset's key-value pairs.

buildFilterSql() - Method in class net.sf.basedb.core.FilterBatcher

Builds the insert SQL statement.

buildInsert(String, Dialect) - Static method in class net.sf.basedb.core.BatchUtil

Build insert SQL string and put it in the SQL map.

buildInsertSelectSql(String) - Method in class net.sf.basedb.core.FilterBatcher

Build the INSERT INTO ...

buildInsertSelectSql(String) - Method in class net.sf.basedb.core.MappingBatcher

Build the INSERT INTO ...

buildInsertSelectSql(String) - Method in class net.sf.basedb.core.PositionBatcher

Build the INSERT INTO ...

buildInsertSelectSql(String) - Method in class net.sf.basedb.core.PositionExtraValueBatcher

Build the INSERT INTO ...

buildInsertSelectSql(String) - Method in class net.sf.basedb.core.SpotBatcher

Build the INSERT INTO ...

buildInsertSelectSql(String) - Method in class net.sf.basedb.core.SpotExtraValueBatcher

Build the INSERT INTO ...

buildInsertSelectSql(VirtualDb, VirtualTable, VirtualColumn[], String) - Static method in class net.sf.basedb.core.BatchUtil

buildInsertSql() - Method in class net.sf.basedb.core.ReporterCloneBatcher

Builds the insert SQL statement.

buildInsertSql(VirtualDb, VirtualTable, VirtualColumn[], Object[]) - Static method in class net.sf.basedb.core.BatchUtil

buildLockRequest(LockOptions) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

buildPositionSql() - Method in class net.sf.basedb.core.PositionBatcher

Builds the insert SQL statement.

buildPropertyAccess(Class, String) - Method in class net.sf.basedb.core.ExtendedPropertyAccessor

buildRawMappingSql() - Method in class net.sf.basedb.core.MappingBatcher

Builds the insert SQL statement.

buildRawSelectQuery() - Method in class net.sf.basedb.core.ReporterCloneBatcher

buildSelectQuery() - Method in class net.sf.basedb.core.ReporterCloneBatcher

Builds a query that select all reporter properties that should be cloned from the real reporter table.

buildSessionFactory(ServiceSessionControl.SessionFactoryConfiguration) - Method in class net.sf.basedb.core.ServiceSessionControl

Create a session factory for the given configuration.

buildSpotSql() - Method in class net.sf.basedb.core.PositionExtraValueBatcher

Builds the insert SQL statement.

buildSpotSql() - Method in class net.sf.basedb.core.SpotBatcher

Builds the insert SQL statement.

buildSpotSql() - Method in class net.sf.basedb.core.SpotExtraValueBatcher

Builds the insert SQL statement.

buildUpdate(String, Dialect) - Static method in class net.sf.basedb.core.BatchUtil

Build update SQL string and put it in the SQL map.

bulletlist - Variable in class net.sf.basedb.clients.web.taglib.table.CellValue

Bundle - Class in net.sf.basedb.clients.web.resources

Declare the names of resource bundles used by the web client.

Bundle() - Constructor for class net.sf.basedb.clients.web.resources.Bundle

Button - Class in net.sf.basedb.clients.web.taglib

This tag is used to display a clickable button.

Button - Class in net.sf.basedb.clients.web.taglib.table

This tag creates a button on a toolbar.

Button() - Constructor for class net.sf.basedb.clients.web.taglib.Button

Button() - Constructor for class net.sf.basedb.clients.web.taglib.table.Button

Button.ButtonActionWrapper - Class in net.sf.basedb.clients.web.taglib.table

ButtonAction - Interface in net.sf.basedb.clients.web.extensions.toolbar

Actions represented as buttons in a toolbar.

ButtonActionWrapper() - Constructor for class net.sf.basedb.clients.web.taglib.table.Button.ButtonActionWrapper

ButtonBean - Class in net.sf.basedb.clients.web.extensions.toolbar

A simple bean-like implementation of the ButtonAction interface.

ButtonBean() - Constructor for class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean

buttonclass - Variable in class net.sf.basedb.clients.web.taglib.Select

buttonGroup - Variable in class net.sf.basedb.clients.web.taglib.Button

ButtonGroup - Class in net.sf.basedb.clients.web.taglib

This tag is used to group buttons together (horizontally) and make them all have the same size.

ButtonGroup() - Constructor for class net.sf.basedb.clients.web.taglib.ButtonGroup

buttonicon - Variable in class net.sf.basedb.clients.web.taglib.Select

buttons - Variable in class net.sf.basedb.clients.web.taglib.ButtonGroup

The buttons in this group.

buttonstyle - Variable in class net.sf.basedb.clients.web.taglib.Select

buttonTag - Variable in class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRenderer

buttonTag - Variable in class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRendererFactory

buttontitle - Variable in class net.sf.basedb.clients.web.taglib.Select

byId(Class<T>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

byId(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

byMultipleIds(Class<T>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

byMultipleIds(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

byNaturalId(Class<T>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

byNaturalId(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

bySimpleNaturalId(Class<T>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

bySimpleNaturalId(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

ByteArrayWriter - Class in net.sf.basedb.core.migrate

Generic writer implementation that writes byte-array values from a result set.

ByteArrayWriter(ResultSet, int, Writer, char[], char[][]) - Constructor for class net.sf.basedb.core.migrate.ByteArrayWriter

bytes - Variable in class net.sf.basedb.core.data.DataCubeData

bytes - Variable in class net.sf.basedb.core.data.DataCubeExtraValueData

bytes - Variable in class net.sf.basedb.core.data.DataCubeFilterData

bytes - Variable in class net.sf.basedb.core.data.DataCubeLayerData

bytes - Variable in class net.sf.basedb.core.data.DiskUsageData

bytes - Variable in class net.sf.basedb.core.data.ExperimentData

bytes - Variable in class net.sf.basedb.core.data.RawBioAssayData

bytes - Variable in class net.sf.basedb.core.data.ReporterCloneTemplateData

bytes - Variable in class net.sf.basedb.core.FilterBatcher

The number of bytes this batcher has added to the experiment.

bytes - Variable in class net.sf.basedb.core.MappingBatcher

The number of bytes this batcher has added to the experiment.

bytes - Variable in class net.sf.basedb.core.PositionBatcher

The number of bytes this batcher has added to the data cube and experiment.

bytes - Variable in class net.sf.basedb.core.PositionExtraValueBatcher

The number of bytes this batcher has added to the experiment.

bytes - Variable in class net.sf.basedb.core.RawDataBatcher

The number of bytes the spot data is occupying on disk.

bytes - Variable in class net.sf.basedb.core.SpotBatcher

The number of bytes this batcher has added to the experiment.

bytes - Variable in class net.sf.basedb.core.SpotExtraValueBatcher

The number of bytes this batcher has added to the experiment.

BYTES_REGEXP - Static variable in class net.sf.basedb.util.Values

bytesPerRow - Variable in class net.sf.basedb.core.FilterBatcher

The number of bytes used by a single row.

bytesPerRow - Variable in class net.sf.basedb.core.MappingBatcher

The number of bytes used by a single row.

bytesPerRow - Variable in class net.sf.basedb.core.PositionBatcher

The number of bytes used by a single row.

bytesPerRow - Variable in class net.sf.basedb.core.PositionExtraValueBatcher

The number of bytes used by a single row.

bytesPerRow - Variable in class net.sf.basedb.core.ReporterCloneBatcher

The number of bytes used by a single row.

bytesPerRow - Variable in class net.sf.basedb.core.SpotBatcher

The number of bytes used by a single row.

bytesPerRow - Variable in class net.sf.basedb.core.SpotExtraValueBatcher

The number of bytes used by a single row.

bzip - Variable in class net.sf.basedb.util.zip.Bzip2FilePacker

Bzip2FilePacker - Class in net.sf.basedb.util.zip

This class wraps the TarFilePacker in a BZIP2 stream, creating a tar.bz2 file.

Bzip2FilePacker() - Constructor for class net.sf.basedb.util.zip.Bzip2FilePacker

Create a new packer that compresses files with the BZIP2 format.

Bzip2FileUnpacker - Class in net.sf.basedb.plugins

A plugin for unpacking a bzip2 compressed file to the BASE file system.

Bzip2FileUnpacker() - Constructor for class net.sf.basedb.plugins.Bzip2FileUnpacker

C

c - Variable in enum class net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType

CABINET - Static variable in class net.sf.basedb.core.Hardware

The id for the HardwareType object representing a cabinet.

cache - Variable in class net.sf.basedb.clients.web.ExperimentExplorer

The cache of reporter ids matching the current reporter filter.

cache - Static variable in class net.sf.basedb.core.DerivedBioAssay.FixDerivedBioAssayParentsRecursivelyAction

cache - Variable in class net.sf.basedb.core.hibernate.AbstractQueryCache

cache - Static variable in class net.sf.basedb.core.MeasuredBioMaterial.RemainingQuantityAction

We need a single action per DbControl and BioMaterial

cache - Variable in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper

cache - Variable in class net.sf.basedb.util.bfs.BaseInputStreamLocator

cache - Variable in class net.sf.basedb.util.listable.TransformCache

cache - Variable in class net.sf.basedb.util.overview.cache.NodeCache

cache - Variable in class net.sf.basedb.util.StaticCache.CleanupTask

Cache() - Constructor for class net.sf.basedb.util.AnnotationUtil.Cache

cacheBase - Variable in class net.sf.basedb.clients.web.servlet.PlotServlet

cacheChildNodes(Node) - Method in class net.sf.basedb.util.overview.GenericOverview

cacheControl - Variable in class net.sf.basedb.clients.web.servlet.CacheControlFilter

cacheControl - Variable in class net.sf.basedb.clients.web.servlet.ImageRemapFilter

CacheControlFilter - Class in net.sf.basedb.clients.web.servlet

This is a filter that sets the "Cache-Control" header in the http response.

CacheControlFilter() - Constructor for class net.sf.basedb.clients.web.servlet.CacheControlFilter

cachedPaths - Variable in class net.sf.basedb.core.Metadata

cachedRssNews - Variable in class net.sf.basedb.clients.web.servlet.RssNewsFeed

CacheEntry(long, Set<Integer>) - Constructor for class net.sf.basedb.util.listable.TransformCache.CacheEntry

cacheFile - Variable in class net.sf.basedb.util.StreamCacher

cacheKey - Variable in class net.sf.basedb.util.overview.cache.DirectionalCacheKey

cacheKey - Variable in class net.sf.basedb.util.overview.cache.IndexedCacheKey

CacheKey(int, String) - Constructor for class net.sf.basedb.util.units.UnitCache.CacheKey

CacheKey(String, Item, Item, SyncFilter.SourceItemTransform, SortedSet<Integer>) - Constructor for class net.sf.basedb.util.listable.TransformCache.CacheKey

cacheNewNode(Object, Node, ChildNodeDirection) - Method in class net.sf.basedb.util.overview.node.NodeFactory

Store a node in the node cache if the current overview context supports caching.

cacheOut - Variable in class net.sf.basedb.util.StreamCacher

cacheQuery(String, Query<?>) - Method in class net.sf.basedb.core.hibernate.AbstractQueryCache

Cache a query.

cacheRegion - Variable in class net.sf.basedb.util.listable.SourceItemTransformerWithCache

cacheRegion - Variable in class net.sf.basedb.util.listable.SourceItemTransformerWithCache.TransformerWithCache

cacheRegion - Variable in class net.sf.basedb.util.listable.TransformCache.CacheKey

cacheReporterData() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

Loads and caches reporter data in an internal structure for quick access.

cacheResults - Variable in class net.sf.basedb.core.AbstractHqlQuery

If the results should be cached or not.

calculateBoxAndWhiskerStatistics(List<Float>) - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet

Creates a box-and-whisker data holder for the given list of values.

calculateIntensities(RawData) - Method in interface net.sf.basedb.util.IntensityCalculator

Calculate intensities from a raw data spot.

calculateIntensities(RawData) - Method in class net.sf.basedb.util.IntensityCalculatorUtil.JepIntensityCalculatorImpl

calculateWeights(List<LowessNormalization.SpotData>, double, List<Double>) - Static method in class net.sf.basedb.plugins.LowessNormalization

CalendarButton - Class in net.sf.basedb.clients.web.taglib

A special button tag that is used to display a "Calendar" button that opens a popup for selecting a date and time.

CalendarButton() - Constructor for class net.sf.basedb.clients.web.taglib.CalendarButton

call() - Method in class net.sf.basedb.core.QueryExecutor.FutureItem

call() - Method in class net.sf.basedb.core.QueryExecutor.FutureResultSet

call() - Method in class net.sf.basedb.core.QueryExecutor.FutureScrollIterator

call() - Method in class net.sf.basedb.core.QueryExecutor.FutureUpdate

call() - Method in class net.sf.basedb.plugins.LowessNormalization.CallableWorker

CallableWorker(List<LowessNormalization.SpotData>, MACalculator, float, float, int, int) - Constructor for class net.sf.basedb.plugins.LowessNormalization.CallableWorker

calledFrom - Variable in class net.sf.basedb.util.StaticCache.State

canAdd(BioWell) - Method in enum class net.sf.basedb.core.BioWell.LockMode

Is it allowed to add (a different) biomaterial to the well?

canAdd(BioWellData) - Method in enum class net.sf.basedb.core.BioWell.LockMode

canAddBioMaterial() - Method in class net.sf.basedb.core.BioWell

Check if it is possible to add/change biomaterial in this well.

cancel() - Method in class net.sf.basedb.clients.jobagent.JobQueueChecker

cancel() - Method in interface net.sf.basedb.core.QueryExecutor.Cancelable

cancel() - Method in class net.sf.basedb.core.QueryExecutor.CancelableSession

cancel() - Method in class net.sf.basedb.core.QueryExecutor.CancelableStatelessSession

cancel() - Method in class net.sf.basedb.core.QueryExecutor.CancelableStatement

cancel() - Method in class net.sf.basedb.util.timer.ThreadTimerTask

CancelableSession(Session) - Constructor for class net.sf.basedb.core.QueryExecutor.CancelableSession

CancelableStatelessSession(StatelessSession) - Constructor for class net.sf.basedb.core.QueryExecutor.CancelableStatelessSession

CancelableStatement(Statement) - Constructor for class net.sf.basedb.core.QueryExecutor.CancelableStatement

cancelQuery() - Method in class net.sf.basedb.core.hibernate.SessionWrapper

cancelQuery() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

Cancels the currently executing query in the same manner as Session.cancelQuery().

canClear(BioWell) - Method in enum class net.sf.basedb.core.BioWell.LockMode

Is it allowed to clear a well from biomaterial?

canClear(BioWellData) - Method in enum class net.sf.basedb.core.BioWell.LockMode

canClearBioMaterial() - Method in class net.sf.basedb.core.BioWell

Check if it is possible to clear the current biomaterial in this well.

canEnumerate - Variable in enum class net.sf.basedb.core.Type

canEnumerate() - Method in enum class net.sf.basedb.core.Type

If it makes sense to use values of this type as an enumeration to choose from.

canLogValues(String) - Method in class net.sf.basedb.core.log.EntityLogOptions

Check if it is allowed to log the old and new values of a modified property.

canUseColoring - Variable in enum class net.sf.basedb.core.Formula.Type

canUseColoring() - Method in enum class net.sf.basedb.core.Formula.Type

If a formula of this type can use coloring or not.

CAPACITANCE - Static variable in class net.sf.basedb.core.Quantity

The id for the Quantity object representing capacitance.

CaseExpression - Class in net.sf.basedb.core.query

An SQL case expression:

CaseExpression(Expression, WhenStatement...) - Constructor for class net.sf.basedb.core.query.CaseExpression

caseInsensitive - Variable in enum class net.sf.basedb.core.FeatureIdentificationMethod

If the feature identifiers may be affect by case sensitivity at the database level or not.

caseInsensitive - Variable in class net.sf.basedb.core.RawDataBatcher

If case should be ignored when comparing strings (external ID)

caseInsensitive() - Method in enum class net.sf.basedb.core.FeatureIdentificationMethod

Return TRUE if this identification method can be case insensitive.

caseInsensitiveComparison() - Method in interface net.sf.basedb.core.dbengine.DbEngine

If the database does case sensitive or case insensitive string comparison in expressions.

caseInsensitiveComparison() - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine

Returns TRUE.

caseInsensitiveComparison() - Method in class net.sf.basedb.core.dbengine.MySQLEngine

Returns TRUE.

caseInsensitiveComparison() - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine

Returns FALSE.

caseWhen(Expression, WhenStatement...) - Static method in class net.sf.basedb.core.query.Expressions

Create a conditional CASE-WHEN expression:

castToDate(String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine

castToDate(String) - Method in interface net.sf.basedb.core.dbengine.DbEngine

Get a function that casts a date/timestamp to a date (eg. no time should be included in the result).

catalog - Variable in class net.sf.basedb.core.hibernate.SchemaExistsWork

catalog - Variable in class net.sf.basedb.core.hibernate.TableExistsWork

categories - Variable in class net.sf.basedb.core.data.AnnotationTypeData

category - Variable in class net.sf.basedb.clients.web.SubContext

categoryColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

Column mapping parameter for assigning annotation types to categories.

categoryMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

CdfFileReporterImporter - Class in net.sf.basedb.plugins

This plug-in can import probesets from Affymetrix CDF files as reporters.

CdfFileReporterImporter() - Constructor for class net.sf.basedb.plugins.CdfFileReporterImporter

Constructor should be empty.

CdfValidationAction - Class in net.sf.basedb.util.affymetrix

Action for validation of CDF files in a file set.

CdfValidationAction(DbControl, ArrayDesign) - Constructor for class net.sf.basedb.util.affymetrix.CdfValidationAction

Create a new action.

CdfValidationFactory - Class in net.sf.basedb.util.affymetrix

Action factory for creating CDF file validators.

CdfValidationFactory() - Constructor for class net.sf.basedb.util.affymetrix.CdfValidationFactory

CdfValidator - Class in net.sf.basedb.util.affymetrix

Helper class for working with Affymetrix CDF files.

CdfValidator() - Constructor for class net.sf.basedb.util.affymetrix.CdfValidator

Create a new instance.

Cell - Class in net.sf.basedb.clients.web.taglib.table

This tag defines a new cell in a row.

Cell() - Constructor for class net.sf.basedb.clients.web.taglib.table.Cell

cellClass - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

cellClass - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

cellStyle - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

cellStyle - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

CellStyleCreator - Class in net.sf.basedb.util.excel

Helper class for keeping track of formatting styles that has been created for given Excel worksheet.

CellStyleCreator(Workbook) - Constructor for class net.sf.basedb.util.excel.CellStyleCreator

Creates a new style creator for the given Excel workbook.

cellType - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil.CellTypeWithInfo

CellTypeWithInfo() - Constructor for class net.sf.basedb.util.excel.XlsxToCsvUtil.CellTypeWithInfo

CellValue - Class in net.sf.basedb.clients.web.taglib.table

This tag adds a value to a cell in a row.

CellValue() - Constructor for class net.sf.basedb.clients.web.taglib.table.CellValue

CelValidationAction - Class in net.sf.basedb.util.affymetrix

Action for validation of CEL files in a file set.

CelValidationAction(DbControl, RawBioAssay) - Constructor for class net.sf.basedb.util.affymetrix.CelValidationAction

Create a new action.

CelValidationFactory - Class in net.sf.basedb.util.affymetrix

Action factory for creating CEL file validators.

CelValidationFactory() - Constructor for class net.sf.basedb.util.affymetrix.CelValidationFactory

CelValidator - Class in net.sf.basedb.util.affymetrix

Helper class for working with Affymetrix CEL files.

CelValidator() - Constructor for class net.sf.basedb.util.affymetrix.CelValidator

Create a new instance.

cfg - Static variable in class net.sf.basedb.core.HibernateUtil

The Hibernate configuration, including all mappings.

cfg - Variable in class net.sf.basedb.core.MigrateRbaToDba.SubtypeMapping

CFResultIterator(SqlResultIterator, SqlResultIterator) - Constructor for class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator

CFSqlResult() - Constructor for class net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult

ch - Variable in class net.sf.basedb.util.importer.spotdata.MatrixSpotIntensityEventHandler

ch - Variable in class net.sf.basedb.util.importer.spotdata.SerialSpotIntensityEventHandler

ch1 - Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData

ch1 - Variable in class net.sf.basedb.plugins.MedianRatioNormalization.SpotData

ch2 - Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData

ch2 - Variable in class net.sf.basedb.plugins.MedianRatioNormalization.SpotData

chain - Variable in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper

chain - Variable in class net.sf.basedb.util.listable.SourceItemTransformerChain

CHAIN_ORDER - Static variable in class net.sf.basedb.core.SyncFilter

chained - Variable in class net.sf.basedb.core.Job.ProgressReporterImpl

ChainedFilter(List<QueryRuntimeFilter>) - Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.ChainedFilter

Create a new ChainedFilter object.

ChainedFilter(QueryRuntimeFilter...) - Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.ChainedFilter

Create a new ChainedFilter object.

chainedProgress - Variable in class net.sf.basedb.util.export.spotdata.BfsExporter

ChainedProgressReporter - Class in net.sf.basedb.util

An implementation of the ProgressReporter interface that chains to another progress reporter while recalculating the percentage values.

ChainedProgressReporter(ProgressReporter) - Constructor for class net.sf.basedb.util.ChainedProgressReporter

Create a new chained progress reporter.

change - Variable in class net.sf.basedb.clients.web.SubContext

Change(ChangeType) - Constructor for enum class net.sf.basedb.core.AnnotationBatcher.Change

changeCurrentSubContext(DbControl, Item, ServletRequest) - Static method in class net.sf.basedb.clients.web.Base

Change the current subcontext depending on the parameters in the request.

ChangeHistory - Class in net.sf.basedb.core

ChangeHistory(ChangeHistoryDetailData) - Constructor for class net.sf.basedb.core.ChangeHistory

CHANGEHISTORY - Enum constant in enum class net.sf.basedb.core.Item

The item is a ChangeHistory entry.

CHANGEHISTORY_VALUES - Enum constant in enum class net.sf.basedb.core.Item

Virtual item representing the new and old values column in ChangeHistory which need special access permissions.

ChangeHistory.TransactionInfo - Class in net.sf.basedb.core

Holds information about a single transaction.

ChangeHistoryData - Class in net.sf.basedb.core.data

Represents the changes made in a single transaction.

ChangeHistoryData() - Constructor for class net.sf.basedb.core.data.ChangeHistoryData

ChangeHistoryDetailData - Class in net.sf.basedb.core.data

Represents a change (creation/update/deletion) made to a single entity in a transaction.

ChangeHistoryDetailData() - Constructor for class net.sf.basedb.core.data.ChangeHistoryDetailData

ChangeHistoryDetailLoader - Class in net.sf.basedb.clients.web.plugins

Data loader implementation for old and new values in the change history which are protected by special permissions.

ChangeHistoryDetailLoader(boolean) - Constructor for class net.sf.basedb.clients.web.plugins.ChangeHistoryDetailLoader

ChangeHistoryItemLoader - Class in net.sf.basedb.clients.web.plugins

Data loader implementation for loading the changed item.

ChangeHistoryItemLoader() - Constructor for class net.sf.basedb.clients.web.plugins.ChangeHistoryItemLoader

ChangeHistoryUtil - Class in net.sf.basedb.clients.web

Utility class for working with change history.

ChangeHistoryUtil() - Constructor for class net.sf.basedb.clients.web.ChangeHistoryUtil

changeHost(URI) - Method in class net.sf.basedb.util.uri.ConnectionParameters

If the connection parameters include a specific host:port or root path a new URI is created were the host:port is replaced and the root path is added to the URI path.

changeInfo - Variable in class net.sf.basedb.core.data.ChangeHistoryDetailData

changeReferenceFactorAndOffset(double, double) - Method in class net.sf.basedb.core.Unit

Changes the factor and offset used for converting values in this unit into the reference unit.

changeReferenceFactorAndOffset(SessionControl, Session, UnitData, double, double) - Static method in class net.sf.basedb.core.Unit

changes - Variable in class net.sf.basedb.core.log.LoggingInterceptor

changeType - Variable in class net.sf.basedb.core.data.ChangeHistoryDetailData

changeType - Variable in class net.sf.basedb.core.log.EntityDetails

changeType - Variable in class net.sf.basedb.core.log.ManualLogEntry

ChangeType - Enum Class in net.sf.basedb.core.log

Enumeration that represents the type of change that has happened.

ChangeType(int, String) - Constructor for enum class net.sf.basedb.core.log.ChangeType

ChangeTypeFormatter - Class in net.sf.basedb.core.log

Formatter implementation that converts an integer into it's ChangeType representation and the uses name() as the formatted value.

ChangeTypeFormatter() - Constructor for class net.sf.basedb.core.log.ChangeTypeFormatter

Create a new formatter.

ChangeTypeFormatter(String) - Constructor for class net.sf.basedb.core.log.ChangeTypeFormatter

Create a new formatter.

channel - Variable in class net.sf.basedb.core.RawDataProperty

channel(int) - Method in class net.sf.basedb.util.jep.ChannelFunction

Get the value of the specified channel of the current sql result.

channel(int) - Method in class net.sf.basedb.util.jep.RawChannelFunction

Get the value of the specified channel of the current sql result.

channel(int, String, Formatter<?>) - Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory

Create a simple dynamic field that exports the channel intensity of the given channel.

ChannelFunction - Class in net.sf.basedb.util.jep

A JEP function class that adds a ch(int) function to a JEP expression parser.

ChannelFunction() - Constructor for class net.sf.basedb.util.jep.ChannelFunction

Create a new instance of this function.

ChannelFunction(int[], IntensityTransform) - Constructor for class net.sf.basedb.util.jep.ChannelFunction

Create a new instance of this function which can be used to dynamically evaluate expressions.

channelIntensity(int) - Static method in class net.sf.basedb.core.VirtualColumn

Get a column that returns the intensity values for a channel.

channelParameters - Variable in class net.sf.basedb.plugins.JepIntensityTransformer

channelRaw(int) - Static method in class net.sf.basedb.core.VirtualColumn

Get a column that stores the raw spot value for a channel.

channels - Variable in class net.sf.basedb.core.data.FormulaData

channels - Variable in class net.sf.basedb.core.data.PlatformData

channels - Variable in class net.sf.basedb.core.data.PlatformVariantData

channels - Variable in class net.sf.basedb.core.RawDataType

channels - Variable in class net.sf.basedb.util.importer.spotdata.GenericIntensityParser

channels - Variable in class net.sf.basedb.util.importer.spotdata.SecondPassSectionSpotsParser

channelToIndex - Variable in class net.sf.basedb.util.jep.ChannelFunction

channelToIndex - Variable in class net.sf.basedb.util.jep.RawChannelFunction

CHAR_ESCAPE - Variable in class net.sf.basedb.core.migrate.postgres.PostgresResultWriterFactory

char64(char) - Static method in class net.sf.basedb.util.bcrypt.BCrypt

Look up the 3 bits base64-encoded by the specified character, range-checking againt conversion table

characterEncoding - Variable in class net.sf.basedb.clients.web.servlet.CharacterEncodingFilter

CharacterEncodingFilter - Class in net.sf.basedb.clients.web.servlet

This is a filter that sets the character encoding for both the request and the response.

CharacterEncodingFilter() - Constructor for class net.sf.basedb.clients.web.servlet.CharacterEncodingFilter

characterSetColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.FileImporter

characterSetMapper - Variable in class net.sf.basedb.plugins.batchimport.FileImporter

CHARGE - Static variable in class net.sf.basedb.core.Quantity

The id for the Quantity object representing electrical charge.

charset - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload

The charset used for decoding header lines.

charset - Variable in class net.sf.basedb.core.data.FileData

charset - Variable in class net.sf.basedb.util.charset.CharsetDetector

charset - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil

charset - Variable in class net.sf.basedb.util.FileImportInputStream

charset - Variable in class net.sf.basedb.util.gtf.GtfInputStream

charset - Variable in class net.sf.basedb.util.uri.UriMetadata

CHARSET_PARAMETER - Static variable in class net.sf.basedb.plugins.util.Parameters

The name of the parameter that is created by Parameters.charsetParameter(String, String, String, boolean)

CharsetDetector - Class in net.sf.basedb.util.charset

Utility class for testing if a text stream can be parsed using a given character set.

CharsetDetector(Charset) - Constructor for class net.sf.basedb.util.charset.CharsetDetector

Create a detector for the given character set that only detects technical issues.

CharsetDetector(Charset, StringDetector) - Constructor for class net.sf.basedb.util.charset.CharsetDetector

Create a detector for the given character set that uses technical an content-based detection.

charsetParameter(String, String, String) - Static method in class net.sf.basedb.plugins.util.Parameters

charsetParameter(String, String, String, boolean) - Static method in class net.sf.basedb.plugins.util.Parameters

Parameter definition that asks for the character encoding used in the file that is imported.

CharsetTesterThread(Charset) - Constructor for class net.sf.basedb.core.File.CharsetTesterThread

charsetType - Static variable in class net.sf.basedb.plugins.util.Parameters

Enumerates all available character sets.

CharsetUtil - Class in net.sf.basedb.util.charset

Helper class for working with charsets and enabling the UTF-8 with fallback charsets: X-UTF-8_with_ISO-8859-1_fallback X-UTF-8_with_windows-1252_fallback

CharsetUtil() - Constructor for class net.sf.basedb.util.charset.CharsetUtil

charsetWithFallbacksType - Static variable in class net.sf.basedb.plugins.util.Parameters

Enumerates all available character sets and also inlcude fallback type.

chart - Variable in class net.sf.basedb.util.plot.HistogramPlot

chart - Variable in class net.sf.basedb.util.plot.ScatterPlot

checkAbortAndDelay() - Method in class net.sf.basedb.clients.web.fileupload.FileUpload

Check if upload has been aborted.

checkAllowedSource(BioMaterial, boolean) - Method in class net.sf.basedb.core.BioMaterialEvent

Check if the biomaterial is allowed as a source.

checkAndCreateTables() - Method in class net.sf.basedb.core.BioAssaySet

checkAndLoadClass(ClassLoader, String, boolean, Class<C>, Class<?>...) - Static method in class net.sf.basedb.util.ClassUtil

Check if a specified class exists and, optionally, if it has public no-argument constructor and implements a set of specific interfaces or superclasses.

checkBatchAnnotatableUsage(boolean, boolean) - Method in class net.sf.basedb.core.BasicItem

Annotatable items that are used with the AnnotationBatcher must not call Annotatable.getAnnotationSet() in the same transaction.

checkBioAssay(DbControl, int, int) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo

Checks that the bioassay with the given id exists in the database.

checkBioMaterialInWell(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.BioPlateValidator

Check that the main type and subtype of the biomaterial is matching the requirements of the bioplate type.

checkBoundary(byte[], int, byte[], int) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload

Check if the given line matches the boundary.

checkClass(Class<?>, boolean, Class<?>...) - Static method in class net.sf.basedb.util.ClassUtil

Check if a specified class has public no-argument constructor and implements a set of specific interfaces or superclasses.

checkClosed() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile

Check if the file has been closed and throws an IllegalStateException if it has.

checkColumnMapping(String, boolean, String) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

Check if a column mapping is a valid mapping expression and optionally if it is complex mapping.

checkColumnMapping(FlatFileParser, String, boolean, String) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

Checks the syntax column mapping and verifies that the given file parser has found the columns that are used in the file.

checkContext(DbControl, ItemQuery<PluginDefinition>, ItemQuery<PluginConfiguration>, GuiContext, Object) - Static method in class net.sf.basedb.util.ContextUtil

Call the InteractivePlugin.isInContext(GuiContext, Object) method for all plug-ins returned by the queries.

checkCoordinate(MappingCoordinate, int, PlateGeometryData, boolean) - Method in class net.sf.basedb.core.PlateMapping

Checks that the coordinate is within the bouds given by the mapping and geometry.

checkDerivedBioAssaySubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.DerivedBioAssayValidator

Check the subtype of the derived bioassay that is the parent to a child derived bioassay.

checked - Variable in class net.sf.basedb.clients.web.taglib.Input

TRUE if the input element is checked.

checkEntity(IdentifiableData) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper

checkEntityArray(Object[]) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper

checkEntityCollection(Collection<?>) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper

checkExperimentArrayDesign(DbControl, OverviewContext, Node, ArrayDesign) - Method in class net.sf.basedb.util.overview.validator.ArrayDesignValidator

Check if an experiment has used more than one array design.

checkExtractOnBioAssay(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.ExtractValidator

checkExtractSubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.DerivedBioAssayValidator

Check the subtype of the extract that is the linked with a derived bioassay.

checkExtractSubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.PhysicalBioAssayValidator

Check the subtype of the extract that is the parent to a physical bioassay.

checkExtractTag(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.ExtractValidator

Check the tag of the child extract in relation to a parent extract.

checkForInvalidNumberOperation() - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine

Returns FALSE.

checkForInvalidNumberOperation() - Method in interface net.sf.basedb.core.dbengine.DbEngine

If we need to check for invalid arguments to numerical functions to avoid exceptions from the database.

checkForInvalidNumberOperation() - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine

Returns TRUE.

checkForJobs() - Method in class net.sf.basedb.clients.jobagent.JobQueueChecker

checkForSignals() - Method in class net.sf.basedb.core.signal.EnhancedThreadSignalHandler

If at least one signal has been received a SignalReceivedException is thrown.

checkForSignals() - Method in class net.sf.basedb.core.signal.ProgressReporterSignalHandler

If at least one signal has been received a SignalReceivedException is thrown.

checkIfDifferent(Object, Unit) - Method in class net.sf.basedb.core.Annotation

Check if the given value is different from the values already stored in this annotation.

checkIfDifferent(List<?>, Unit) - Method in class net.sf.basedb.core.Annotation

Check if the given values are different from the values already stored in this annotation.

checkIfReportersExists(FusionCDFData, ReporterBatcher, boolean, ReporterType, ProgressReporter) - Method in class net.sf.basedb.util.affymetrix.CdfValidator

Verify if probesets in a CDF file exists as reporters and optionally create those that doesn't exists.

checkImportable(SessionControl, PluginDefinition, PluginConfiguration, File, String, GuiContext, Object) - Static method in class net.sf.basedb.util.AutoDetectFileFormat

checkInstallation(DbControl, Collection<PluginInfo>) - Static method in class net.sf.basedb.core.PluginDefinition

Check the installation status of the given list of plug-ins.

checkInternalJobQueue() - Method in class net.sf.basedb.core.InternalJobQueue

checkInterrupted() - Static method in class net.sf.basedb.core.signal.ThreadSignalHandler

Utility method to check if the current thread has been interrupted and (may) throw a SignalException if it has.

checkInterval - Variable in class net.sf.basedb.clients.jobagent.Agent

checkItemType(Item) - Method in class net.sf.basedb.core.ItemSubtype

Check if this subtype can be used on items of the given type.

checkJdbcDriver(String, String, String) - Static method in class net.sf.basedb.core.HibernateUtil

Check that a JDBC driver is registered and try to load a driver if not.

checkLine(int, String) - Method in class net.sf.basedb.util.charset.SimpleStringDetector

checkLine(int, String) - Method in interface net.sf.basedb.util.charset.StringDetector

Check the given line.

checkLocked(String) - Method in class net.sf.basedb.core.Application.StartupOptions

checkLocked(String) - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration

Check that the

checkMagicNumber(PushbackInputStream, byte[]) - Static method in class net.sf.basedb.util.FileUtil

Take a peek at an input stream and check if the first few bytes matches the bCheck parameter.

checkManualMembersAllowed() - Method in class net.sf.basedb.core.ItemList

checkMax(int, String, int) - Static method in class net.sf.basedb.core.IntegerUtil

Check that an integer is equal or lower than a maximum value.

checkMd5 - Variable in class net.sf.basedb.core.File.UploadStream

If the md5 should be checked or not.

checkMemberType(Collection<ItemList>) - Method in class net.sf.basedb.core.ItemList

Checks that the lists have the same member type as this list.

checkMemberType(Item) - Method in class net.sf.basedb.core.ItemList

Checks if the other type is the same type as the member type of this list.

checkMin(int, String, int) - Static method in class net.sf.basedb.core.IntegerUtil

Check that an integer is equal or greater than a minimum value.

checkMinMax(int, String, int, int) - Static method in class net.sf.basedb.core.IntegerUtil

Check that an integer is equal or between a minimum and a maximum value.

checkModified() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile

Check if the underlying file has been modified since it was last processed.

checkNext - Variable in class net.sf.basedb.core.DynamicResultIterator

checkNext - Variable in class net.sf.basedb.util.extensions.ActionIterator

checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ChannelFunction

checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ExtraValueFunction

checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.FunctionSafeJep.UnknownFunction

checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.InReporterListFunction

checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.LeftFunction

checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.Log2Function

checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.MeanFunction

checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.NotInReporterListFunction

checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.PositionFunction

checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.RawChannelFunction

checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.RawFunction

checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ReporterFunction

checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ScoreFunction

checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.SimpleJepFunction

checkNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.ColFunction

checkNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.DataNoFunction

checkNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.DefaultItemFunction

checkNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.LineNoFunction

checkParentBioSourceSubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.SampleValidator

Check the subtype of the biosurce that is the parent to a sample.

checkParentExtractSubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.ExtractValidator

Check the subtype of the extract that is the parent to another extract.

checkParentSampleSubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.ExtractValidator

Check the subtype of the sample that is the parent to an extract.

checkParentSampleSubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.SampleValidator

Check the subtype of the sample that is the parent to another sample.

checkPassword(String, String) - Static method in class net.sf.basedb.core.User

Check the plain-text password against the crypted password.

checkPermission(Permission) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

checkPermission(Permission) - Method in interface net.sf.basedb.core.AccessControlled

Check if the logged in user has the desired permission on the item, otherwise throw an exception.

checkPermission(Permission) - Method in class net.sf.basedb.core.BasicBatcher

Checks if the logged in user has the specified permission on this item.

checkPermission(Permission) - Method in class net.sf.basedb.core.BasicItem

Checks if the logged in user has the specified permission on this item.

checkPermission(Permission) - Method in class net.sf.basedb.core.BioMaterialEventSource

checkPermission(Permission) - Method in class net.sf.basedb.core.Coloring

checkPermission(Permission, String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

For checking the permission and adding a custom message to the PermissionDeniedException if the required permission is missing.

checkPhysicalBioAssaySubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.DerivedBioAssayValidator

Check the subtype of the physical bioassay that is the parent to a derived bioassay.

checkpw(String, String) - Static method in class net.sf.basedb.util.bcrypt.BCrypt

Check that a plaintext password matches a previously hashed one

checkSameArrayDesign(Collection<RawBioAssay>, boolean) - Static method in class net.sf.basedb.util.IntensityCalculatorUtil

checkSuperclass - Variable in class net.sf.basedb.util.formatter.MultiFormatter

checkSyncFiltersAllowed() - Method in class net.sf.basedb.core.ItemList

checkTimeoutOnRemoteSlots() - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager

Check the remote slots to see if they have timed out.

checkUniqueFields(String, String) - Method in class net.sf.basedb.plugins.executor.BaseFileExporterSupport

checkUniqueFields(String, String) - Method in class net.sf.basedb.plugins.executor.BfsExporterSupport

checkUnsafeScriptableUsage(Extension<?>) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Checks if the given extension may violate the 'Content Security Policy' for the server.

checkUnsafeScriptableUsage(ExtensionsFile) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Checks if the given extensions file contain any extensions that may violate the 'Content Security Policy' for the server.

checkUnsafeScriptableUsageInternal(Extension<?>) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

checkValues - Variable in class net.sf.basedb.core.ParameterType

child - Variable in class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator

child - Variable in class net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult

child - Variable in class net.sf.basedb.core.QueryRuntimeFilterFactory.ChildFilter

The item type of the child item.

child - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay

child - Variable in class net.sf.basedb.util.importer.spotdata.SecondPassSectionSpotsParser

CHILD_DESCRIPTION - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

The name of the parameter that asks for the description of the child bioassay set.

CHILD_DESCRIPTION - Static variable in class net.sf.basedb.plugins.util.Parameters

The name of the parameter that asks is created by Parameters.childDescriptionParameter(String, String, String)

CHILD_NAME - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

The name of the parameter that asks for the name of the child bioassay set.

CHILD_NAME - Static variable in class net.sf.basedb.plugins.util.Parameters

The name of the parameter that is created by Parameters.childNameParameter(String, String, String)

CHILD_TO_PARENT - Enum constant in enum class net.sf.basedb.core.SyncFilter.SourceItemTransform

Source items are transformed to parent items.

CHILD_TO_PARENT - Static variable in class net.sf.basedb.util.listable.ToBioSourceSourceItemTransformerFactory

CHILD_TO_PARENT - Static variable in class net.sf.basedb.util.listable.ToDerivedBioAssaySourceItemTransformerFactory

CHILD_TO_PARENT - Static variable in class net.sf.basedb.util.listable.ToExtractSourceItemTransformerFactory

CHILD_TO_PARENT - Static variable in class net.sf.basedb.util.listable.ToPhysicalBioAssaySourceItemTransformerFactory

CHILD_TO_PARENT - Static variable in class net.sf.basedb.util.listable.ToRawBioAssaySourceItemTransformerFactory

CHILD_TO_PARENT - Static variable in class net.sf.basedb.util.listable.ToSampleSourceItemTransformerFactory

childAssays - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo

ChildBioAssay() - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay

Create a new object.

ChildBioAssay(int) - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay

Create a new object

childCreationEvents - Variable in class net.sf.basedb.core.data.BioMaterialData

childDescriptionParameter(String, String, String) - Static method in class net.sf.basedb.plugins.util.Parameters

Create a plugin parameter that asks for the description of the child bioassay set.

childErrors - Variable in class net.sf.basedb.util.overview.Node

ChildFilter(Item, Item) - Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.ChildFilter

Create a new ChildFilter object.

childHasDifferentReporterPositionMapping - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo

childId - Variable in class net.sf.basedb.core.data.keyring.GroupGroups

ChildItem - Class in net.sf.basedb.core

An abstract base class for all items which are child items to a Shareable parent item.

ChildItem(BasicData) - Constructor for class net.sf.basedb.core.ChildItem

childIterator - Variable in class net.sf.basedb.util.Tree.EntryIterator

An iterator over the children of the root entry.

childNameParameter(String, String, String) - Static method in class net.sf.basedb.plugins.util.Parameters

Create a plugin parameter that asks for the name of the child bioassay set.

ChildNodeDirection - Enum Class in net.sf.basedb.util.overview.node

Represents the direction to use for loading child nodes in a tree.

ChildNodeDirection(boolean, boolean, boolean) - Constructor for enum class net.sf.basedb.util.overview.node.ChildNodeDirection

ChildNodeLoaderAction - Interface in net.sf.basedb.util.overview.extensions

Load and create child nodes for a given parent node.

children - Variable in class net.sf.basedb.core.data.BioAssayData

children - Variable in class net.sf.basedb.core.data.BioMaterialData

children - Variable in class net.sf.basedb.core.data.DerivedBioAssayData

children - Variable in class net.sf.basedb.core.data.GroupData

children - Variable in class net.sf.basedb.core.data.PlateData

children - Variable in class net.sf.basedb.util.listable.CollectExtracts

children - Variable in class net.sf.basedb.util.overview.Node

children - Variable in class net.sf.basedb.util.Tree.Entry

childrenLoaded - Variable in class net.sf.basedb.util.overview.Node

childReporterPositions - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo

childToParent - Variable in class net.sf.basedb.util.listable.AbstractSourceItemTransformerFactory

childToParentChain(List<SourceItemTransformer>, Item, Item, boolean) - Static method in class net.sf.basedb.util.listable.ToExtractSourceItemTransformerFactory

Utility method for creating the transformer chain from child items up to extracts.

childWarnings - Variable in class net.sf.basedb.util.overview.Node

chIndex - Variable in class net.sf.basedb.util.importer.spotdata.MatrixSpotIntensityEventHandler

chIndex - Variable in class net.sf.basedb.util.importer.spotdata.SerialSpotIntensityEventHandler

chooseClientAlias(String[], Principal[], Socket) - Method in class net.sf.basedb.util.ssl.StaticKeyManager

chooseServerAlias(String, Principal[], Socket) - Method in class net.sf.basedb.util.ssl.StaticKeyManager

CIRCULAR_REFERENCE - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for circular references among pooled items.

CircularRefInfo(DbControl, Identifiable) - Constructor for class net.sf.basedb.core.Trashcan.CircularRefInfo

city - Variable in class net.sf.basedb.util.GeoLocation

classes - Static variable in class net.sf.basedb.core.ExtendedProperties

A list with the name attribute of all classes found in the xml file.

classLoader - Variable in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration

classLoader - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtension

classLoader - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint

classLoaders - Variable in class net.sf.basedb.util.extensions.xml.XmlLoader

classLoaders - Static variable in class net.sf.basedb.util.JarClassLoader

A map of all loaded class loaders.

ClassLocal<E> - Class in net.sf.basedb.util

This class is a similar to the JDK ThreadLocal class, but stores one object per class instead of one object per thread.

ClassLocal() - Constructor for class net.sf.basedb.util.ClassLocal

Create a new ClassLocal object.

ClassMapErrorHandler - Class in net.sf.basedb.util.error

Error handler that allows the registration of one or more error handler for subclasses to Throwable.

ClassMapErrorHandler(ErrorHandler) - Constructor for class net.sf.basedb.util.error.ClassMapErrorHandler

Create a new ClassMapErrorHandler.

classMetadata - Variable in class net.sf.basedb.core.Metadata

className - Variable in class net.sf.basedb.core.data.PluginDefinitionData

className - Variable in class net.sf.basedb.util.extensions.manager.PluginInfoKey

className - Variable in class net.sf.basedb.util.extensions.xml.PluginInfo

classNameToPath(String) - Method in class net.sf.basedb.util.JarClassLoader

Convert a class name to a file path.

classPath - Variable in class net.sf.basedb.util.JarClassLoader

Contains mappings from class names to the JAR file in which the class implementation can be found.

ClassUtil - Class in net.sf.basedb.util

Utility class for Class objects.

ClassUtil() - Constructor for class net.sf.basedb.util.ClassUtil

clazz - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

clazz - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

clazz - Variable in class net.sf.basedb.clients.web.extensions.login.FieldInfo

clazz - Variable in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

clazz - Variable in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean

clazz - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory

clazz - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory

clazz - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean

clazz - Variable in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean

clazz - Variable in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory

clazz - Variable in class net.sf.basedb.clients.web.taglib.ExceptionCatcher

clazz - Variable in class net.sf.basedb.clients.web.taglib.StylableTag

clazz - Variable in class net.sf.basedb.clients.web.taglib.tab.Tab

Optional class attribute.

clazz - Variable in class net.sf.basedb.clients.web.taglib.table.Cell

Optional class attribute

clazz - Variable in class net.sf.basedb.clients.web.taglib.table.CellValue

clazz - Variable in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter

clazz - Variable in class net.sf.basedb.core.Metadata.BasicItem2DataPropertyPath

clazz - Variable in class net.sf.basedb.core.Metadata

clazz - Variable in class net.sf.basedb.core.Metadata.NoopPropertyPath

clazz - Variable in class net.sf.basedb.core.ParameterType

The class of allowed parameter values.

clazz - Variable in class net.sf.basedb.core.QueryExecutor.FutureItem

clazz - Variable in class net.sf.basedb.util.extensions.events.ActionClassEventFilter

clazz - Variable in class net.sf.basedb.util.filter.InstanceOfFilter

clean() - Method in class net.sf.basedb.util.listable.TransformCache

clean(AnnotationBatcher.UpdateBatcher) - Method in class net.sf.basedb.core.MigrateRbaToDba.Rba

Remove links to from the raw bioassay to annotations, files, etc.

cleanable - Variable in class net.sf.basedb.core.DbControl.State

cleanable - Variable in class net.sf.basedb.util.StaticCache.LockSafeInputStream

cleanable - Variable in class net.sf.basedb.util.StaticCache.LockSafeOutputStream

cleanContextFromProperty(Session, Item, String, String, boolean) - Static method in class net.sf.basedb.core.Update

cleaner - Static variable in class net.sf.basedb.core.Application

For keeping track of objects that need to be cleaned up.

cleanSessionControlCache(boolean) - Static method in class net.sf.basedb.core.Application

Clean the cache from unused SessionControl objects.

cleanUp() - Method in class net.sf.basedb.core.DbControl

Clear and close all objects.

cleanUp(FileFilter) - Method in class net.sf.basedb.util.StaticCache

Remove all files that matches the specified filter from the cache.

cleanupProjectSpecificAnnotations() - Static method in class net.sf.basedb.core.ProjectSpecificAnnotationsManager

Delete project-specific annotations that belong to projects that no longer exists.

cleanUpTask(FileFilter) - Method in class net.sf.basedb.util.StaticCache

Creates a task that cleans up this cache when it is executed.

CleanupTask(StaticCache, FileFilter) - Constructor for class net.sf.basedb.util.StaticCache.CleanupTask

clear() - Method in class net.sf.basedb.core.AbstractResultList

Not supported.

clear() - Method in class net.sf.basedb.core.hibernate.SessionWrapper

clear() - Method in class net.sf.basedb.core.snapshot.SnapshotManager

Clear the manager from all memory-cached information.

clear() - Method in class net.sf.basedb.core.UnmodifiableResultList

Not supported.

clear() - Method in class net.sf.basedb.util.AnnotationUtil.Cache

Clear all information from the cache.

clear() - Method in class net.sf.basedb.util.formatter.LookupFormatter

Remove all registered lookup entries.

clear() - Method in class net.sf.basedb.util.Tree

Clear all elements except the root element.

clear(Session) - Static method in class net.sf.basedb.core.HibernateUtil

Clear the session of cached objects.

clearAllRecent() - Method in class net.sf.basedb.core.ItemContext

Clear all recently used values lists.

clearDbControlCache() - Method in class net.sf.basedb.core.SessionControl

clearError() - Method in class net.sf.basedb.util.extensions.ActionIterator

Clear any error that has been registered for the current action.

clearError() - Method in class net.sf.basedb.util.extensions.ExtensionContext

clearError() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext

clearError() - Method in class net.sf.basedb.util.extensions.InvokationContext

Clear the registered error for the current extension or extension point.

clearError() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension

clearError() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint

clearErrorList(JEP) - Static method in class net.sf.basedb.util.jep.Jep

This is a workaround for a bug in the JEP error handling.

clearErrors - Variable in class net.sf.basedb.util.extensions.ExtensionsInvoker

clearExecuteCommand() - Method in class net.sf.basedb.core.Job

Reset the currently stored execution command to force a plug-in to restart from the beginning instead of at the stored breakpoint.

clearFailures() - Method in class net.sf.basedb.util.overview.Node

Clear all warnings, errors on this node and on all child nodes.

clearLog() - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog

Clear the log.

clearRecent(String) - Method in class net.sf.basedb.core.ItemContext

Clear the recently used values list.

clearRecent(Item) - Method in class net.sf.basedb.core.ItemContext

Clear the recently used items list from items of the specified type.

clearRecent(Item, String) - Method in class net.sf.basedb.core.ItemContext

Clear the recently used items sublist from items of the specified type.

clearRecent(Item, ItemSubtype) - Method in class net.sf.basedb.core.ItemContext

Clear the recently used items list from items of the specified type.

clearSources() - Method in class net.sf.basedb.core.BioMaterialEvent

Clear the sources collection and return the used quantities to the source biomaterials.

clearSourcesExcept(BioMaterial) - Method in class net.sf.basedb.core.BioMaterialEvent

Clear the sources collection and return the used quantities to the source biomaterials, except for the given biomaterial.

clearState - Variable in class net.sf.basedb.core.PluginResponse

clearUsableUnits() - Method in class net.sf.basedb.core.AnnotationType

Clear all units.

clearValueConverters() - Method in class net.sf.basedb.util.extensions.xml.XmlLoader

Remove all value converters.

client - Variable in class net.sf.basedb.core.data.ChangeHistoryData

client - Variable in class net.sf.basedb.core.data.ClientDefaultSettingData

client - Variable in class net.sf.basedb.core.data.ContextData

client - Variable in class net.sf.basedb.core.data.ContextIndex

client - Variable in class net.sf.basedb.core.data.HelpData

client - Variable in class net.sf.basedb.core.data.SessionData

client - Variable in class net.sf.basedb.core.data.UserClientSettingData

client - Variable in class net.sf.basedb.core.data.UserDeviceData

client - Variable in class net.sf.basedb.core.SessionControl

Information about the ClientData that created this SessionControl.

client - Variable in class net.sf.basedb.plugins.HelpImporter

Client - Class in net.sf.basedb.core

This class represents a registered client application.

Client(ClientData) - Constructor for class net.sf.basedb.core.Client

CLIENT - Enum constant in enum class net.sf.basedb.core.Item

The item is an Client.

CLIENT_RUNTIME_FILTER - Static variable in class net.sf.basedb.core.UserClientSetting

This filter will only return items if the logged in user has generic read permission to clients.

clientCertificate - Variable in class net.sf.basedb.core.data.FileServerData

clientCertificate - Variable in class net.sf.basedb.util.uri.ConnectionParameters

clientCertificatePassword - Variable in class net.sf.basedb.util.uri.ConnectionParameters

clientContext - Variable in class net.sf.basedb.util.extensions.ExtensionPointContext

clientContext - Variable in class net.sf.basedb.util.extensions.ExtensionsInvoker

ClientContext - Class in net.sf.basedb.util.extensions

Keeps information about the current context in the client application that extensions can use to decide what actions to generate.

ClientContext() - Constructor for class net.sf.basedb.util.extensions.ClientContext

Create a new context with no session or current item.

ClientContext(DbControl) - Constructor for class net.sf.basedb.util.extensions.ClientContext

Create a new context with a DbControl.

ClientContext(DbControl, Object) - Constructor for class net.sf.basedb.util.extensions.ClientContext

Create a new context with a DbControl and item.

ClientContext(SessionControl) - Constructor for class net.sf.basedb.util.extensions.ClientContext

Create a new context with a session and no DbControl.

ClientContext(SessionControl, Object) - Constructor for class net.sf.basedb.util.extensions.ClientContext

Create a new context with a session and item but no DbControl.

ClientContext(SessionControl, DbControl, Object) - Constructor for class net.sf.basedb.util.extensions.ClientContext

ClientData - Class in net.sf.basedb.core.data

This class holds information about a client.

ClientData() - Constructor for class net.sf.basedb.core.data.ClientData

ClientDefaultSetting - Class in net.sf.basedb.core

This class is used to represent a setting for specific client application.

ClientDefaultSetting(ClientDefaultSettingData) - Constructor for class net.sf.basedb.core.ClientDefaultSetting

CLIENTDEFAULTSETTING - Enum constant in enum class net.sf.basedb.core.Item

The item is an ClientDefaultSetting.

ClientDefaultSettingData - Class in net.sf.basedb.core.data

ClientDefaultSettingData() - Constructor for class net.sf.basedb.core.data.ClientDefaultSettingData

clientDefaultSettings - Variable in class net.sf.basedb.core.SessionControl

Stores name and value from ClientDefaultSettingData.

clientId - Variable in class net.sf.basedb.core.data.ChangeHistoryData

clientId - Variable in class net.sf.basedb.core.log.TransactionDetails

ClientInfo(int, String, String) - Constructor for class net.sf.basedb.core.SessionControl.ClientInfo

clientItem - Static variable in class net.sf.basedb.plugins.HelpExporter

clientItem - Static variable in class net.sf.basedb.plugins.HelpImporter

clientParameter - Variable in class net.sf.basedb.plugins.HelpExporter

clientParameter - Variable in class net.sf.basedb.plugins.HelpImporter

clientPassword - Variable in class net.sf.basedb.core.data.FileServerData

clientSettings - Variable in class net.sf.basedb.core.data.UserData

clientType - Variable in class net.sf.basedb.plugins.HelpExporter

clonableProperty(ClonableProperty) - Static method in class net.sf.basedb.core.VirtualColumn

Get a virtual column view of a cloned reporter property.

ClonableProperty - Class in net.sf.basedb.core

Represents a reporter property that can be cloned to a per-experiment table in the dynamic database.

ClonableProperty(String, String, String, String, Type, int, boolean, Formula.AverageMethod, boolean) - Constructor for class net.sf.basedb.core.ClonableProperty

Create a cloned property representation of a static property.

ClonableProperty(String, ReporterClonePropertyData) - Constructor for class net.sf.basedb.core.ClonableProperty

Create a cloned property representation of a data-layer object.

ClonableProperty(ExtendedProperty) - Constructor for class net.sf.basedb.core.ClonableProperty

Create a cloned property representation of an extended property

ClonableReporterQuery - Interface in net.sf.basedb.core

An interface that indicates that a query may be used together with cloned reporter information.

CLONAL_AMPLIFICATION - Static variable in class net.sf.basedb.core.PhysicalBioAssay

The id for the PhysicalBioAssayType item representing a flow cell.

clone - Variable in class net.sf.basedb.util.annotations.InheritSpecification

cloneCachedNode(Object, Node, ChildNodeDirection) - Method in class net.sf.basedb.util.overview.node.NodeFactory

Clones a cached node if the current context supports caching and another node with the given cache key already exists.

CLONED - Enum constant in enum class net.sf.basedb.core.Annotation.Source

The annotation is an inherited annotation with a local copy of the values at the time the copy was made.

CLONED_REPORTERS - Enum constant in enum class net.sf.basedb.core.VirtualTable

Table that holds cloned reporter information for an experiment.

cloneParameter(PluginParameter<T>, T) - Static method in class net.sf.basedb.plugins.util.Parameters

Clone a plug-in parameter but give it a different default value.

cloneParameterWithDefaultValue(PluginParameter<T>) - Method in class net.sf.basedb.core.plugin.AbstractPlugin

Clone a plug-in parameter and set the default value to the value that is already stored in the job or configuration parameters.

cloneReporters(ReporterCloneBatcher.CloneSource, ReporterCloneTemplate, ProgressReporter) - Method in class net.sf.basedb.core.ReporterCloneBatcher

Create a reporter clone table in the dynamic database for this experiment and populate it with the current reporter annotations for all reporters that are part of the experiment.

CloneReportersPlugin - Class in net.sf.basedb.plugins

A plug-in that clone reporter annotations to an experiment.

CloneReportersPlugin() - Constructor for class net.sf.basedb.plugins.CloneReportersPlugin

CloneSource() - Constructor for enum class net.sf.basedb.core.ReporterCloneBatcher.CloneSource

close() - Method in class net.sf.basedb.clients.jobagent.executors.DummyJobExecutor

close() - Method in class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor

close() - Method in class net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor

close() - Method in class net.sf.basedb.clients.jobagent.handlers.AbstractCustomRequestHandler

close() - Method in interface net.sf.basedb.clients.jobagent.handlers.CustomRequestHandler

This method is called at when the agent is stopped.

close() - Method in class net.sf.basedb.clients.jobagent.handlers.MultiProtocolRequestHandler

Close this handler.

close() - Method in interface net.sf.basedb.clients.jobagent.JobExecutor

This method is called at when the agent is stopped or paused.

close() - Method in class net.sf.basedb.clients.jobagent.slotmanager.InternalSlotManager

close() - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager

close() - Method in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager

close() - Method in interface net.sf.basedb.clients.jobagent.slotmanager.SlotManager

This method is called when the job agent is shutting down.

close() - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Shut down the extensions system.

close() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper

close() - Static method in class net.sf.basedb.clients.web.extensions.service.Services

Stop all services.

close() - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate

Do nothing.

close() - Method in class net.sf.basedb.clients.web.plugins.XlsxTemplate

Dispose and close workbook.

close() - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate

Do nothing.

close() - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator

close() - Method in class net.sf.basedb.core.AbstractBatcher

close() - Method in class net.sf.basedb.core.AnnotationBatcher.InsertBatcher

Close the batcher.

close() - Method in class net.sf.basedb.core.AnnotationBatcher.UpdateBatcher

Close the batcher.

close() - Method in interface net.sf.basedb.core.Batcher

Flush the batcher and close it.

close() - Method in class net.sf.basedb.core.DataResultIterator

From the ResultIterator interface ---------------------------------

close() - Method in class net.sf.basedb.core.DbControl

Close the connection to the database.

close() - Method in class net.sf.basedb.core.DynamicResultIterator

From the ResultIterator interface ---------------------------------

close() - Method in class net.sf.basedb.core.File.CharsetTesterThread

The file has been uploaded.

close() - Method in class net.sf.basedb.core.File.UploadStream

Close the stream and register the size and location with the file item.

close() - Method in class net.sf.basedb.core.hibernate.SessionWrapper

close() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

close() - Method in class net.sf.basedb.core.InternalJobQueue

Cleanup

close() - Method in class net.sf.basedb.core.ItemResultIterator

From the ResultIterator interface ---------------------------------

close() - Method in class net.sf.basedb.core.plugin.ExportOutputStream

close() - Method in interface net.sf.basedb.core.query.ResultIterator

Close the iterator and immediately release all resources associated with it.

close() - Method in class net.sf.basedb.core.ReporterScoreResultIterator

From the ResultIterator interface ---------------------------------

close() - Method in class net.sf.basedb.core.ScrollIterator

Close the results and return resources.

close() - Method in class net.sf.basedb.core.SessionControl

Close this session control so it can't be used again.

close() - Method in class net.sf.basedb.util.bfs.AnnotationParser

close() - Method in interface net.sf.basedb.util.bfs.BfsParser

Close the parser and relase underlying system resources that are associated with it.

close() - Method in class net.sf.basedb.util.bfs.DataParser

close() - Method in class net.sf.basedb.util.bfs.MetadataParser

close() - Method in class net.sf.basedb.util.excel.XlsxTableWriter

Closes the workbook unless it was supplied in the constructor from an external source.

close() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil

Closes the current workbook.

close() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.WorkbookStream

close() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile

Close the writeable file.

close() - Method in class net.sf.basedb.util.gtf.GtfInputStream

close() - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser

close() - Method in class net.sf.basedb.util.InputStreamCombiner

Closes all underlying streams.

close() - Method in class net.sf.basedb.util.InputStreamSplitter

close() - Method in class net.sf.basedb.util.InputStreamTracker

close() - Method in class net.sf.basedb.util.jobagent.JobAgentConnection

Close the connection to the job agent.

close() - Method in class net.sf.basedb.util.jobagent.JobAgentServerConnection

Stop listening for incoming connections.

close() - Method in class net.sf.basedb.util.StaticCache.LockSafeInputStream

close() - Method in class net.sf.basedb.util.StaticCache.LockSafeOutputStream

close() - Method in class net.sf.basedb.util.StreamCacher

Close the master stream and remove the cached file data.

close() - Method in class net.sf.basedb.util.uri.CloseResourceInputStream

Make sure the client connection manager is closed when the file has been completely downloaded.

close() - Method in class net.sf.basedb.util.zip.Bzip2FilePacker

Finish the BZIP stream.

close() - Method in interface net.sf.basedb.util.zip.FilePacker

End the packing and close.

close() - Method in class net.sf.basedb.util.zip.GzipFilePacker

Finish the GZIP stream.

close() - Method in class net.sf.basedb.util.zip.TarFilePacker

Finish the TAR file.

close() - Method in class net.sf.basedb.util.zip.ZipFilePacker

Finish the ZIP file.

close(int) - Method in class net.sf.basedb.clients.web.util.SimpleSignalProgressReporter

close(int) - Method in class net.sf.basedb.core.signal.AbstractSignalReceiver

Close this signal receiver.

close(int) - Method in class net.sf.basedb.core.signal.LocalSignalReceiver

close(int) - Method in interface net.sf.basedb.core.signal.SignalReceiver

Close the receiver.

close(int) - Method in class net.sf.basedb.core.signal.SocketSignalReceiver

Close this receiver and the socket it is listening on.

close(Closeable) - Static method in class net.sf.basedb.util.FileUtil

Close a Closeable without throwing an exception.

close(InputStream) - Static method in class net.sf.basedb.util.FileUtil

Close an input stream without throwing an exception.

close(InputStream) - Static method in class net.sf.basedb.util.SocketUtil

Close an InputStream without throwing any exceptions.

close(OutputStream) - Static method in class net.sf.basedb.util.FileUtil

Close an output stream without throwing an exception.

close(Reader) - Static method in class net.sf.basedb.util.SocketUtil

Close a Reader without throwing any exceptions.

close(Writer) - Static method in class net.sf.basedb.util.SocketUtil

Close a Writer without throwing any exceptions.

close(AutoCloseable) - Static method in class net.sf.basedb.util.FileUtil

Close a AutoCloseable without throwing an exception.

close(ServerSocket) - Static method in class net.sf.basedb.util.SocketUtil

Close a server socket without throwing any exceptions.

close(Socket) - Static method in class net.sf.basedb.util.SocketUtil

Close a socket without throwing any exceptions.

close(ServerSocketChannel) - Static method in class net.sf.basedb.util.SocketUtil

Close a server socket channel without throwing any exceptions.

close(Session) - Static method in class net.sf.basedb.core.HibernateUtil

Close a session.

close(StatelessSession) - Static method in class net.sf.basedb.core.HibernateUtil

Close a statless session.

closed - Variable in class net.sf.basedb.core.File.UploadStream

If this file closed or not.

closed - Variable in class net.sf.basedb.core.SessionControl

If the session control has been closed it can no longer be used.

closed - Variable in class net.sf.basedb.util.StaticCache.LockSafeInputStream

closed - Variable in class net.sf.basedb.util.StaticCache.LockSafeOutputStream

closeJobExecutor() - Method in class net.sf.basedb.clients.jobagent.Agent

Close the job executor.

closeJobQueueChecker() - Method in class net.sf.basedb.clients.jobagent.Agent

Close the job queue checker.

closeLogFile() - Method in class net.sf.basedb.core.plugin.AbstractPlugin

Close the log file created by AbstractPlugin.createLogFile(String).

CloseMyDbControl(RelatedItemHelper) - Constructor for class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper.CloseMyDbControl

CloseResourceInputStream - Class in net.sf.basedb.util.uri

Inputstream filter that closes a given resource whenever the parent input stream is closed.

CloseResourceInputStream(InputStream, Closeable) - Constructor for class net.sf.basedb.util.uri.CloseResourceInputStream

Create a new stream.

closeResultSet(ResultSet, String) - Method in class net.sf.basedb.core.AbstractSqlQuery

Close the result set without throwing an exception.

closeServer() - Method in class net.sf.basedb.clients.jobagent.Agent

Close the service listener.

closeSlotManager() - Method in class net.sf.basedb.clients.jobagent.Agent

Close the slot manager.

closeStatement(Statement, String) - Method in class net.sf.basedb.core.AbstractSqlQuery

Close the statement without throwing an exception.

closeTimeout - Variable in class net.sf.basedb.clients.jobagent.Agent

Timeout to wait for jobs to act on the ABORT signal when stopping.

closeTimeout - Variable in class net.sf.basedb.core.InternalJobQueue

Timeout to wait for jobs to act on the ABORT signal when shutting down BASE.

CLUSTER_GENERATION - Static variable in class net.sf.basedb.core.Kit

The ID for the cluster generation (in a flow cell) kit type, for example a protocol used when creating a PhysicalBioAssay.

CLUSTER_GENERATION - Static variable in class net.sf.basedb.core.Protocol

The ID for the cluster generation (in a flow cell) protocol type, for example a protocol used when creating a PhysicalBioAssay.

CLUSTER_GENERATOR - Static variable in class net.sf.basedb.core.Hardware

The id for the HardwareType object representing a cluster generator station.

cmap - Variable in class net.sf.basedb.util.AnnotationUtil.Cache

cmd - Variable in class net.sf.basedb.clients.jobagent.CmdLine

CmdLine - Class in net.sf.basedb.clients.jobagent

Utility class for parsing command line arguments.

CmdLine(String[]) - Constructor for class net.sf.basedb.clients.jobagent.CmdLine

Create a new object for parsing the command line.

coalesce(String...) - Static method in class net.sf.basedb.core.StringUtil

Return the first non-null value (or null if all values are null).

colFunction - Variable in class net.sf.basedb.util.parser.JepMapper

ColFunction - Class in net.sf.basedb.util.parser

Adds a col() function to Jep.

ColFunction(List<String>, NumberFormat) - Constructor for class net.sf.basedb.util.parser.ColFunction

ColFunction(List<String>, NumberFormat, Formatter<Date>) - Constructor for class net.sf.basedb.util.parser.ColFunction

ColFunction(Map<String, Integer>, NumberFormat) - Constructor for class net.sf.basedb.util.parser.ColFunction

ColFunction(Map<String, Integer>, NumberFormat, Formatter<Date>) - Constructor for class net.sf.basedb.util.parser.ColFunction

colIndex - Variable in class net.sf.basedb.clients.web.plugins.DynamicQueryWrapper

collect(Item, Set<Integer>) - Method in class net.sf.basedb.util.listable.TransformContext

Store collected items for later use if collecting has been enabled.

CollectChildren(boolean, boolean) - Constructor for class net.sf.basedb.util.listable.CollectExtracts.CollectChildren

collectChildrenOfCollected(boolean) - Method in class net.sf.basedb.util.listable.CollectExtracts

The created transformer collect the ID:s of all child extracts to the already collected extracts and store them in the CollectExtracts.getCollectedChildren().

collectChildrenOfSource(boolean) - Method in class net.sf.basedb.util.listable.CollectExtracts

The created transformer collect the ID:s of all child extracts to the source extracts and store them in the CollectExtracts.getCollectedChildren().

collected - Variable in class net.sf.basedb.util.listable.CollectExtracts

collectedByItemType - Variable in class net.sf.basedb.util.listable.TransformContext

collectedExtracts - Variable in class net.sf.basedb.util.listable.CollectedExtractsToDerivedBioAssayTransformer

collectedExtracts - Variable in class net.sf.basedb.util.listable.CollectedExtractsToRawBioAssayTransformer

collectedExtracts - Variable in class net.sf.basedb.util.listable.DerivedBioAssayToRawBioAssayTransformer

collectedExtracts - Variable in class net.sf.basedb.util.listable.ExtractToParentExtractTransformer

collectedExtracts - Variable in class net.sf.basedb.util.listable.PhysicalBioAssayToDerivedBioAssayTransformer

CollectedExtractsToDerivedBioAssayTransformer - Class in net.sf.basedb.util.listable

Source item transformer implementation that transform collected extract items to derived bioassays.

CollectedExtractsToDerivedBioAssayTransformer(CollectExtracts) - Constructor for class net.sf.basedb.util.listable.CollectedExtractsToDerivedBioAssayTransformer

Create a new collected extracts to derived bioassay transformer.

CollectedExtractsToDerivedBioAssayTransformer(CollectExtracts, boolean) - Constructor for class net.sf.basedb.util.listable.CollectedExtractsToDerivedBioAssayTransformer

Create a new collected extracts to derived bioassay transformer.

CollectedExtractsToRawBioAssayTransformer - Class in net.sf.basedb.util.listable

Source item transformer implementation that transform collected extract items to raw bioassays.

CollectedExtractsToRawBioAssayTransformer(CollectExtracts) - Constructor for class net.sf.basedb.util.listable.CollectedExtractsToRawBioAssayTransformer

Create a new collected extracts to derived bioassay transformer.

CollectExtracts - Class in net.sf.basedb.util.listable

Collect extracts seen on derived bioassays and raw bioassays that has been loaded by other transformers.

CollectExtracts() - Constructor for class net.sf.basedb.util.listable.CollectExtracts

Create a new derived bioassay to physical bioassay transformer.

CollectExtracts.CollectChildren - Class in net.sf.basedb.util.listable

Transformer implementation that collect the child extracts from the source or collected extracts.

CollectExtracts.CollectFromDerivedBioAssays - Class in net.sf.basedb.util.listable

Transformer implementation that given a set of derived bioassays load their linked extracts and store that in the parent class.

CollectExtracts.CollectFromExtracts - Class in net.sf.basedb.util.listable

Transformer implementation that store the given set of extracts in the parent class.

CollectExtracts.CollectFromRawBioAssays - Class in net.sf.basedb.util.listable

Transformer implementation that given a set of raw bioassays load their linked extracts and store that in the parent class.

CollectExtracts.CollectParents - Class in net.sf.basedb.util.listable

Transformer implementation that collect the parent extracts from the source or collected extracts.

CollectExtracts.ResetCollected - Class in net.sf.basedb.util.listable

Transformer implementation that reset the collected extracts before forwarding the call to the parent transformer.

collectFromDerivedBioAssays(boolean) - Method in class net.sf.basedb.util.listable.CollectExtracts

The created transformer collect the ID:s of all extracts linked from the source derived bioassays and then return the same set of derived bioassays again.

CollectFromDerivedBioAssays(boolean) - Constructor for class net.sf.basedb.util.listable.CollectExtracts.CollectFromDerivedBioAssays

collectFromExtracts() - Method in class net.sf.basedb.util.listable.CollectExtracts

The created transformer collect the ID:s of all extracts in the source collection and return same set of extracts again.

CollectFromExtracts() - Constructor for class net.sf.basedb.util.listable.CollectExtracts.CollectFromExtracts

collectFromRawBioAssays() - Method in class net.sf.basedb.util.listable.CollectExtracts

The created transformer collect the ID:s of all extracts linked from the source raw bioassays and then return the same set of raw bioassays again.

CollectFromRawBioAssays() - Constructor for class net.sf.basedb.util.listable.CollectExtracts.CollectFromRawBioAssays

collecting - Variable in class net.sf.basedb.util.listable.TransformContext

COLLECTION_SEPARATOR - Static variable in class net.sf.basedb.clients.web.plugins.SimpleExport

collectionFormatter - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

CollectionFormatter<I> - Class in net.sf.basedb.util.formatter

Formatter implementation that formats a collection of values to a string by concatenating the values with a given separator.

CollectionFormatter(String, boolean, Formatter<? super I>) - Constructor for class net.sf.basedb.util.formatter.CollectionFormatter

CollectionFormatter(Formatter<? super I>) - Constructor for class net.sf.basedb.util.formatter.CollectionFormatter

Create a collection formatting using ", " as separator and skipping null values.

CollectionPropertyPath(Type) - Constructor for class net.sf.basedb.core.Metadata.CollectionPropertyPath

collections - Variable in class net.sf.basedb.util.NestedIterator

The array to iterate.

collectionSeparator - Variable in class net.sf.basedb.clients.web.plugins.PlainTextTemplate

collectionSeparator - Variable in class net.sf.basedb.clients.web.plugins.XlsxTemplate

CollectionTransformer<S,D> - Interface in net.sf.basedb.util.collections

Allows a collection to be transformed by applying some operation to it.

CollectParents(boolean, boolean) - Constructor for class net.sf.basedb.util.listable.CollectExtracts.CollectParents

collectParentsOfCollected(boolean) - Method in class net.sf.basedb.util.listable.CollectExtracts

The created transformer collect the ID:s of all parent extracts to the already collected extracts and store them in the CollectExtracts.getCollectedParents().

collectParentsOfSource(boolean) - Method in class net.sf.basedb.util.listable.CollectExtracts

The created transformer collect the ID:s of all parent extracts to the source extracts and store them in the CollectExtracts.getCollectedParents().

CollectSqlTarget() - Constructor for class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget

CollectSqlTarget(DbEngine, Dialect, SchemaGenerator.Mode, Connection) - Constructor for class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget

colNo - Variable in class net.sf.basedb.util.excel.XlsxTableWriter

colNum - Variable in class net.sf.basedb.clients.web.plugins.PlainTextTemplate

colNum - Variable in class net.sf.basedb.clients.web.plugins.XlsxTemplate

colOffset - Variable in class net.sf.basedb.util.parser.FlatFileParser.ExcelData

color - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup

ColorFormatter - Class in net.sf.basedb.clients.web.formatter

Formatter that adds a small colored box next to a value.

ColorFormatter(ColorGenerator, Formatter<Number>) - Constructor for class net.sf.basedb.clients.web.formatter.ColorFormatter

Create a new color formatter.

colorGen - Variable in class net.sf.basedb.clients.web.formatter.ColorFormatter

ColorGenerator - Class in net.sf.basedb.util

This class is used to generate colors for numerical values.

ColorGenerator(Color, Color, Color, float, float, float, boolean) - Constructor for class net.sf.basedb.util.ColorGenerator

Create a new color generator.

coloring - Variable in class net.sf.basedb.core.data.ExtraValueTypeData

coloring - Variable in class net.sf.basedb.core.data.FormulaData

coloring - Variable in class net.sf.basedb.core.ExtraValueType

coloring - Variable in class net.sf.basedb.core.Formula

Coloring - Class in net.sf.basedb.core

This class keeps coloring information for items which can be colored when values are displayed in a client application.

Coloring() - Constructor for class net.sf.basedb.core.Coloring

Create a new independent coloring object.

Coloring(ColoringData, AccessControlled) - Constructor for class net.sf.basedb.core.Coloring

Create Coloring object which links to an existing item.

ColoringData - Class in net.sf.basedb.core.data

Hold coloring information.

ColoringData() - Constructor for class net.sf.basedb.core.data.ColoringData

ColoringData(boolean, boolean, Float, Float, Float) - Constructor for class net.sf.basedb.core.data.ColoringData

COLORS - Static variable in class net.sf.basedb.clients.web.ExperimentExplorer

Predefined colors for annotation groups

colspan - Variable in class net.sf.basedb.clients.web.taglib.table.Header

column - Variable in class net.sf.basedb.clients.web.extensions.list.ListColumnDataLoader

column - Variable in class net.sf.basedb.core.data.BioWellData

column - Variable in class net.sf.basedb.core.data.FeatureData

column - Variable in class net.sf.basedb.core.data.MappingCoordinate

The column number.

column - Variable in class net.sf.basedb.core.data.PlateCoordinate

The column number.

column - Variable in class net.sf.basedb.core.data.RawData

column - Variable in class net.sf.basedb.core.data.ReporterClonePropertyData

column - Variable in class net.sf.basedb.core.data.WellData

column - Variable in class net.sf.basedb.core.DynamicRestriction

column - Variable in class net.sf.basedb.core.ExtendedProperty

column - Variable in class net.sf.basedb.core.ExtraValueExpression

column - Variable in class net.sf.basedb.core.FeatureCoordinate

The column of this feature.

column - Variable in class net.sf.basedb.core.query.SqlColumnExpression

column - Variable in class net.sf.basedb.core.query.VirtualColumnExpression

column - Variable in class net.sf.basedb.core.RawBioAssayPropertyExpression

column - Variable in class net.sf.basedb.core.ReporterPropertyExpression

column - Variable in class net.sf.basedb.core.VirtualColumn

The column name in the database of the column.

column - Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData

column(VirtualColumn) - Static method in class net.sf.basedb.core.query.Dynamic

Create an expression representing a column in the root table: expression = rootAlias.columnName.

column(VirtualTable, VirtualColumn) - Static method in class net.sf.basedb.core.query.Dynamic

Create an expression representing a column in a table: expression = tableAlias.columnName.

COLUMN - Enum constant in enum class net.sf.basedb.core.ExtraValue.CoordinateType

The extra values are attached to column coordinates only.

COLUMN - Enum constant in enum class net.sf.basedb.core.VirtualTable

Table that maps columns coordinates in a data cube to raw bioassays.

COLUMN - Static variable in class net.sf.basedb.core.VirtualColumn

This column stores the data cube column coordinate.

COLUMN_EXPRESSION - Enum constant in enum class net.sf.basedb.core.Formula.Type

An arbitrary expression that specify one formula only.

COLUMN_EXTRA_FLOAT - Enum constant in enum class net.sf.basedb.core.VirtualTable

Table that stores float column extra values.

COLUMN_EXTRA_INT - Enum constant in enum class net.sf.basedb.core.VirtualTable

Table that stores integer column extra values.

COLUMN_EXTRA_STRING - Enum constant in enum class net.sf.basedb.core.VirtualTable

Table that stores string column extra values.

COLUMN_PREFIX - Static variable in class net.sf.basedb.clients.web.plugins.SimpleExport

COLUMN_RESTRICTION - Enum constant in enum class net.sf.basedb.core.Formula.Type

An arbitraty expression that specify one formula only.

columnColumnMapping - Static variable in class net.sf.basedb.plugins.PlateFlatFileImporter

columnColumnMapping - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

columnColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

columnContent - Variable in class net.sf.basedb.clients.web.taglib.table.Table

columnCount - Variable in class net.sf.basedb.util.bfs.AnnotationWriter

columnCount - Variable in class net.sf.basedb.util.bfs.DataWriter

ColumnDef - Class in net.sf.basedb.clients.web.taglib.table

This tag defines a column in the table.

ColumnDef() - Constructor for class net.sf.basedb.clients.web.taglib.table.ColumnDef

ColumnDef.NullIterator<A,B> - Class in net.sf.basedb.clients.web.taglib.table

Iterator implementation that returns a single null value and nothing more.

columnFilter - Variable in class net.sf.basedb.clients.web.taglib.table.Table

columnFormatter - Variable in class net.sf.basedb.clients.web.taglib.table.Table

columnHeaders - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

columnHeaders - Variable in class net.sf.basedb.util.parser.ColFunction

columnHeaders - Variable in class net.sf.basedb.util.parser.FlatFileParser

List of the column names found by splitting the data header using the data splitter regexp.

ColumnHeaders - Class in net.sf.basedb.clients.web.taglib.table

Generate column headers for the columns that has been defined for this table.

ColumnHeaders() - Constructor for class net.sf.basedb.clients.web.taglib.table.ColumnHeaders

columnId - Variable in class net.sf.basedb.clients.web.taglib.table.Cell

The ID of the column to which this cell belongs.

columnIndex - Variable in class net.sf.basedb.util.bfs.AnnotationModel

ColumnInfo(String, String, Integer, int, boolean, boolean) - Constructor for class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo

Create a new ColumnInfo object.

ColumnKey(Comparable<?>, String) - Constructor for class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey

columnMapper - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter

columnMapper - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

columnMapper - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

ColumnMapper - Class in net.sf.basedb.util.parser

Returns the string found in the column given by the index set in the constructor.

ColumnMapper(int, String) - Constructor for class net.sf.basedb.util.parser.ColumnMapper

Create a new column mapper.

ColumnMapper(int, String, NumberFormat, boolean) - Constructor for class net.sf.basedb.util.parser.ColumnMapper

Deprecated.

In 3.15, use ColumnMapper(int, String, NumberFormat, Formatter, boolean) instead

ColumnMapper(int, String, NumberFormat, Formatter<Date>, boolean) - Constructor for class net.sf.basedb.util.parser.ColumnMapper

Create a new column mapper using a specific number or date format.

columnMappingParameterName - Variable in class net.sf.basedb.plugins.batchimport.PropertyIdMethod

columnName - Variable in class net.sf.basedb.core.Update.DropColumnChange

columnNo - Variable in class net.sf.basedb.core.data.DataCubeColumnData

columns - Variable in class net.sf.basedb.clients.web.taglib.table.Table

Which columns that should be visible and their order

columns - Variable in class net.sf.basedb.core.data.DataCubeData

columns - Variable in class net.sf.basedb.core.data.PlateGeometryData

columns - Variable in class net.sf.basedb.core.dbengine.TableInfo

columns - Variable in class net.sf.basedb.core.dbengine.TableInfo.IndexInfo

columns - Variable in class net.sf.basedb.core.dbengine.TableInfo.PrimaryKeyInfo

columns - Variable in class net.sf.basedb.core.ExtraValueJoin

columns - Variable in enum class net.sf.basedb.core.VirtualTable

The columns in the table.

columns() - Method in class net.sf.basedb.util.parser.FlatFileParser.Data

The number of columns as determined by the FlatFileParser.setDataSplitterRegexp(Pattern) regular expression.

columnSeparator - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil

columnSubtitle - Variable in class net.sf.basedb.clients.web.taglib.table.Table

ColumnSubtitles - Class in net.sf.basedb.clients.web.taglib.table

Generate column subtitle header for the columns that has been defined for this table.

ColumnSubtitles() - Constructor for class net.sf.basedb.clients.web.taglib.table.ColumnSubtitles

CombinedPropertyPath(List<Metadata.PropertyPath>) - Constructor for class net.sf.basedb.core.Metadata.CombinedPropertyPath

CombiningEventFilter - Class in net.sf.basedb.util.extensions.events

Event filter that only passes on events based on multiple other event filters.

CombiningEventFilter(Collection<EventFilter>, boolean) - Constructor for class net.sf.basedb.util.extensions.events.CombiningEventFilter

Create a new combining event filter.

command - Variable in class net.sf.basedb.core.PluginRequest

command - Variable in class net.sf.basedb.core.RequestInformation

command - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper

COMMAND_CONFIGURE_EXTERNAL_PARAMETERS - Static variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

COMMAND_CONFIGURE_IO_JOB - Static variable in interface net.sf.basedb.plugins.executor.IOSupport

This command is sent to import and export plug-ins in the job configuration sequence: InteractivePlugin.getRequestInformation(GuiContext, String) and InteractivePlugin.configure(GuiContext, Request, Response)

COMMAND_CONFIGURE_IO_PLUGIN - Static variable in interface net.sf.basedb.plugins.executor.IOSupport

This command is sent to import and export plug-ins in the plug-in configuration sequence: InteractivePlugin.getRequestInformation(GuiContext, String) and InteractivePlugin.configure(GuiContext, Request, Response)

COMMAND_CONFIGURE_JOB - Static variable in interface net.sf.basedb.core.plugin.Request

This should be the first command to use when setting the plugin's job parameters.

COMMAND_CONFIGURE_PARSER - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

COMMAND_CONFIGURE_PLUGIN - Static variable in interface net.sf.basedb.core.plugin.Request

This should be the first command to use when setting the plugin's configuration.

COMMAND_EXECUTE - Static variable in interface net.sf.basedb.core.plugin.Request

This command will tell the plugin to start its execution.

COMMAND_EXECUTE_IO_JOB - Static variable in interface net.sf.basedb.plugins.executor.IOSupport

This command is sent to import and export plug-ins in the job execution sequence: Plugin.run(Request, Response, ProgressReporter)

COMMAND_MANUAL_CONFIG - Static variable in class net.sf.basedb.plugins.Base1PluginExecuter

This command is used if the user decides to configure the plugin by hand.

COMMAND_SELECT_CONFIGURATIONS - Static variable in class net.sf.basedb.plugins.PluginConfigurationImporter

commandHandlers - Variable in class net.sf.basedb.clients.jobagent.handlers.DefaultRequestHandler

comment - Variable in class net.sf.basedb.core.authentication.LoginRequest

comment - Variable in class net.sf.basedb.core.data.BioMaterialEventData

comment - Variable in class net.sf.basedb.core.data.PlateEventData

comment - Variable in class net.sf.basedb.core.MigrateRbaToDba.LineMapping

commit() - Method in class net.sf.basedb.core.DbControl

Commit all changes made to items and close the connection to the database.

commit(Transaction) - Static method in class net.sf.basedb.core.HibernateUtil

Commit a transaction.

commitQueue - Variable in class net.sf.basedb.core.DbControl

A list of items that need special handling when commit is called.

COMMON - Static variable in class net.sf.basedb.clients.web.resources.Bundle

Resource bundle with strings that are used in lots and lots of places in the web gui.

commonCharsets - Static variable in class net.sf.basedb.core.Config

CommonData - Class in net.sf.basedb.core.data

This is a convenience class that extends the SharedData class and implements the NameableData and RemovableData interfaces.

CommonData() - Constructor for class net.sf.basedb.core.data.CommonData

commonDom - Static variable in class net.sf.basedb.core.PredefinedQuery

Holds the XML document containing the common queries.

CommonItem - Class in net.sf.basedb.core

CommonItem(CommonData) - Constructor for class net.sf.basedb.core.CommonItem

commonName - Variable in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter

commonQueryFile - Static variable in class net.sf.basedb.core.PredefinedQuery

The path to the query file with common queries.

CompactButtonRenderer - Class in net.sf.basedb.clients.web.extensions.toolbar

A compact renderer for toolbar button actions, which only only displays the icon.

CompactButtonRenderer(JspContext) - Constructor for class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRenderer

CompactButtonRendererFactory - Class in net.sf.basedb.clients.web.extensions.toolbar

Factory that create CompactButtonRenderer objects for rendering ButtonAction:s.

CompactButtonRendererFactory() - Constructor for class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRendererFactory

ComparableComparator<T extends Comparable<T>> - Class in net.sf.basedb.util

A comparator implemenation for any Comparable objects.

ComparableComparator() - Constructor for class net.sf.basedb.util.ComparableComparator

compare(String, String) - Method in class net.sf.basedb.util.StringLengthComparator

compare(URI, URI) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager.JarFirstURIComparator

compare(RawDataType, RawDataType) - Method in class net.sf.basedb.core.RawDataTypes.NameComparator

compare(AnnotationSnapshot, AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot.SortByProjectComparator

compare(AnnotationSnapshot, AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot.AnnotationTypeComparator

compare(AnnotationSnapshot, AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot.ProjectComparator

compare(T, T) - Method in class net.sf.basedb.util.ComparableComparator

compare(T, T) - Method in class net.sf.basedb.util.NameableComparator

compare(T, T) - Method in class net.sf.basedb.util.PriorityComparator

compare(T, T) - Method in class net.sf.basedb.util.ToStringComparator

compareByChainOrder() - Static method in class net.sf.basedb.core.SyncFilter

Create a comparator that sorts sync filters by: Filter group Source item type: BIOSOURCE, SAMPLE, EXTRACT, PHYSICALBIOASSAY, DERIVEDBIOASSAY, RAWBIOASSAY Type of transformation: PARENT_TO_CHILD, NONE, CHILD_TO_PARENT Name Source item must exists is sorted before source item must not exist Id

compareTo(ExperimentExplorer.AnnotationGroup) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup

compareTo(ExperimentExplorerPlotServlet.ColumnKey) - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey

The ID of the key determines equality.

compareTo(ClonableProperty) - Method in class net.sf.basedb.core.ClonableProperty

Sort by title, but mandatory properties before non-madatory.

compareTo(KeyPermission) - Method in class net.sf.basedb.core.data.keyring.KeyPermission

Compare the keyId of this object to the keyId of another KeyPermission object.

compareTo(PluginKeys) - Method in class net.sf.basedb.core.data.keyring.PluginKeys

Compare the keyId of this object to the keyId of another PluginKeys object.

compareTo(ProjectPermission) - Method in class net.sf.basedb.core.data.keyring.ProjectPermission

Compare the projectId of this object to the projectId of another ProjectPermission object.

compareTo(TableInfo.ColumnInfo) - Method in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo

compareTo(ItemProxy) - Method in class net.sf.basedb.core.ItemProxy

compareTo(RawDataType) - Method in class net.sf.basedb.core.RawDataType

Compare the id:s of the raw data types.

compareTo(LowessNormalization.SpotData) - Method in class net.sf.basedb.plugins.LowessNormalization.SpotData

Sort by A in ascending order.

compareTo(MedianRatioNormalization.SpotData) - Method in class net.sf.basedb.plugins.MedianRatioNormalization.SpotData

Sort by ratio in ascending order.

compareTo(AnyToAnyLinkStatistics) - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics

Sort items by count, linkName and targetType.

compareTo(ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile

compareTo(Node) - Method in class net.sf.basedb.util.overview.Node

compareTo(PlotAnnotation) - Method in class net.sf.basedb.util.plot.PlotAnnotation

compareTo(UnitCache.CacheKey) - Method in class net.sf.basedb.util.units.UnitCache.CacheKey

compareWith(String) - Static method in class net.sf.basedb.core.Version

Compare the given version string, which should be of the form a.b or a.b.c, with the current BASE version.

compile(boolean, boolean) - Method in class net.sf.basedb.clients.web.extensions.XJspCompiler

Called when a JSP page needs recompiling.

compile(String, HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.CompileAll

Compile all files found in dir, recursively entering subdirectories.

CompileAll - Class in net.sf.basedb.clients.web.servlet

This servlet will scan for all files ending with .jsp and issue a request for them with the parameter jsp_precompile=true therby compiling all JSP files into servlets.

CompileAll() - Constructor for class net.sf.basedb.clients.web.servlet.CompileAll

completed - Variable in class net.sf.basedb.core.SimpleAbsoluteProgressReporter

complexMappings - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter

Parameter that asks if complex column mappings should be enabled or not.

component - Variable in class net.sf.basedb.core.Metadata.ComponentPropertyPath

ComponentData - Interface in net.sf.basedb.core.data

Tagging interface that we need all componenets to implement so that we are able to export them properly using generic code.

ComponentPropertyPath(ComponentType, int, Type) - Constructor for class net.sf.basedb.core.Metadata.ComponentPropertyPath

CompoundMapper - Class in net.sf.basedb.util.parser

A compound mapper that gets its value by invoking multiple other mappers which are set in the constructor.

CompoundMapper(List<Mapper>) - Constructor for class net.sf.basedb.util.parser.CompoundMapper

Create a new compound mapper.

CompoundMapper(List<Mapper>, NumberFormat, boolean) - Constructor for class net.sf.basedb.util.parser.CompoundMapper

Create a new compound mapper, using a specific number formatter as it's parser.

CompoundMapper(List<Mapper>, NumberFormat, Formatter<Date>, boolean) - Constructor for class net.sf.basedb.util.parser.CompoundMapper

Create a new compound mapper, using a specific number formatter as it's parser.

compress - Variable in class net.sf.basedb.core.File.UploadStream

If the file should be compressed or not.

compress(ProgressReporter) - Method in class net.sf.basedb.core.File

Compress the file stored on the disk.

compressed - Variable in class net.sf.basedb.core.data.FileData

compressedSize - Variable in class net.sf.basedb.core.data.FileData

compressOrDecompress(ProgressReporter, boolean) - Method in class net.sf.basedb.core.File

condition - Variable in class net.sf.basedb.core.dbengine.TableInfo.IndexInfo

condition - Variable in class net.sf.basedb.core.HibernateUtil.DelayedFilterDef

condition - Variable in class net.sf.basedb.core.query.WhenStatement

conditionalExpression(Filter<? extends Query>, Expression, Expression) - Static method in class net.sf.basedb.core.query.Expressions

Create an expression that falls back to one of two expression depending on if the query passes a filter or not.

ConditionalQueryElement - Class in net.sf.basedb.core.query

ConditionalQueryElement(Filter<Query>, QueryElement, QueryElement) - Constructor for class net.sf.basedb.core.query.ConditionalQueryElement

conditionalRestriction(Filter<? extends Query>, Restriction, Restriction, boolean) - Static method in class net.sf.basedb.core.query.Restrictions

Create a restriction that falls back to one of two restrictions depending on if the query passes a filter or not.

config - Static variable in class net.sf.basedb.core.Config

Variable for holding the configuration properties.

config - Variable in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget

config - Variable in class net.sf.basedb.core.plugin.ParameterValuesWrapper

config - Variable in class net.sf.basedb.util.ContextUtil.ContextResult

Config - Class in net.sf.basedb.core

Use this class to access the configuration settings for BASE.

Config() - Constructor for class net.sf.basedb.core.Config

configDir - Static variable in class net.sf.basedb.core.Config

configList - Static variable in class net.sf.basedb.plugins.PluginConfigurationExporter

configuration - Variable in class net.sf.basedb.core.ParameterValuesImpl

configuration - Variable in class net.sf.basedb.core.plugin.AbstractPlugin

configuration - Variable in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues

ConfigurationException - Exception in net.sf.basedb.core

This exception is thrown by the Config class if there is a problem with finding or loading the configuration settings.

ConfigurationException(String) - Constructor for exception net.sf.basedb.core.ConfigurationException

Creates a new ConfigurationException.

ConfigurationException(String, Throwable) - Constructor for exception net.sf.basedb.core.ConfigurationException

Creates a new ConfigurationException with a cause.

configurationMap - Variable in class net.sf.basedb.plugins.PluginConfigurationImporter

configurationParameters - Variable in class net.sf.basedb.core.PluginRequest

configurations - Variable in class net.sf.basedb.core.data.PluginDefinitionData

configurationValues - Variable in class net.sf.basedb.core.data.PluginConfigurationData

configure() - Method in class net.sf.basedb.core.PluginConfiguration

Start the configuration sequence for a plugin.

configure(GuiContext) - Method in class net.sf.basedb.core.Job

Start the configuration sequence for a job.

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.clients.web.plugins.SimpleExport

configure(GuiContext, Request, Response) - Method in interface net.sf.basedb.core.plugin.InteractivePlugin

Configure the plugin.

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.Base1PluginExecuter

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

Override this method so that we can make some extra parameter checks: A mapping for 'Value type' must be specified when 'create' or 'create+update' mode is used

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.BfsExporterPlugin

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.CdfFileReporterImporter

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.BaseFileExporterSupport

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.BaseFileImporterSupport

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.BfsExporterSupport

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.BfsImporterSupport

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.FormulaFilter

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.GalExporter

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.HelpExporter

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.HelpImporter

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin

Store configuration settings for Request.COMMAND_CONFIGURE_PLUGIN, and Request.COMMAND_CONFIGURE_JOB.

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.JepExtraValueCalculator

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.JepIntensityTransformer

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.LowessNormalization

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.ManualTransformCreator

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.MedianRatioNormalization

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PackedFileExporter

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PlateFlatFileImporter

Store configuration settings for Request.COMMAND_CONFIGURE_PLUGIN and Request.COMMAND_CONFIGURE_JOB.

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PlateMappingExporter

Store configuration settings for Request.COMMAND_CONFIGURE_PLUGIN and Request.COMMAND_CONFIGURE_JOB.

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PlateMappingImporter

Store configuration settings for Request.COMMAND_CONFIGURE_PLUGIN and Request.COMMAND_CONFIGURE_JOB.

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PluginConfigurationExporter

Store configuration settings for Request.COMMAND_CONFIGURE_JOB.

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PluginConfigurationImporter

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter

Store configuration settings for Request.COMMAND_CONFIGURE_PLUGIN and Request.COMMAND_CONFIGURE_JOB.

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter

Store configuration settings for Request.COMMAND_CONFIGURE_PLUGIN, RawDataFlatFileImporter.COMMAND_CONFIGURE_PARSER and Request.COMMAND_CONFIGURE_JOB.

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter

Store configuration settings for Request.COMMAND_CONFIGURE_PLUGIN and Request.COMMAND_CONFIGURE_JOB.

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

Store configuration settings for Request.COMMAND_CONFIGURE_PLUGIN and Request.COMMAND_CONFIGURE_JOB.

configure(GuiContext, Request, Response) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker

CONFIGURE_IMPORT - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

CONFIGURE_MAPPING - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

CONFIGURE_OPTIONS - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

CONFIGURE_OPTIONS - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

ConfigureByExample - Interface in net.sf.basedb.util.parser

This is a tagging interface for all plugins that use the FlatFileParser and wants easier configuration of the regular expressions used to parse the file.

configureExecutor - Variable in class net.sf.basedb.plugins.executor.BaseFileExporterSupport

configureExecutor - Variable in class net.sf.basedb.plugins.executor.BaseFileImporterSupport

configureExecutor - Variable in class net.sf.basedb.plugins.executor.BfsExporterSupport

configureExecutor - Variable in class net.sf.basedb.plugins.executor.BfsImporterSupport

configureExportImportPluginParameters - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

configureExternalParameters - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

configureImport - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

configureJob - Variable in class net.sf.basedb.clients.web.plugins.SimpleExport

configureJob - Variable in class net.sf.basedb.plugins.Base1PluginExecuter

Holds info about a job configuration request.

configureJob - Variable in class net.sf.basedb.plugins.BaseFileExporterPlugin

configureJob - Variable in class net.sf.basedb.plugins.BfsExporterPlugin

configureJob - Variable in class net.sf.basedb.plugins.CdfFileReporterImporter

configureJob - Variable in class net.sf.basedb.plugins.executor.BaseFileImporterSupport

configureJob - Variable in class net.sf.basedb.plugins.executor.BfsImporterSupport

configureJob - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

configureJob - Variable in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport

configureJob - Variable in class net.sf.basedb.plugins.FormulaFilter

configureJob - Variable in class net.sf.basedb.plugins.GalExporter

configureJob - Variable in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter

configureJob - Variable in class net.sf.basedb.plugins.HelpExporter

configureJob - Variable in class net.sf.basedb.plugins.HelpImporter

configureJob - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter

configureJob - Variable in class net.sf.basedb.plugins.IntensityCalculatorPlugin

configureJob - Variable in class net.sf.basedb.plugins.JepExtraValueCalculator

configureJob - Variable in class net.sf.basedb.plugins.JepIntensityTransformer

configureJob - Variable in class net.sf.basedb.plugins.LowessNormalization

configureJob - Variable in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator

configureJob - Variable in class net.sf.basedb.plugins.ManualTransformCreator

configureJob - Variable in class net.sf.basedb.plugins.MedianRatioNormalization

configureJob - Variable in class net.sf.basedb.plugins.PackedFileExporter

configureJob - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter

configureJob - Variable in class net.sf.basedb.plugins.PlateMappingExporter

configureJob - Variable in class net.sf.basedb.plugins.PlateMappingImporter

configureJob - Variable in class net.sf.basedb.plugins.PluginConfigurationExporter

configureJob - Variable in class net.sf.basedb.plugins.PluginConfigurationImporter

configureJob - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter

configureJob - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

configureJob - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

configureJob - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

configureJob - Variable in class net.sf.basedb.util.zip.AbstractFileUnpacker

configureManual - Variable in class net.sf.basedb.plugins.Base1PluginExecuter

Holds information about a manual plugin configuration request.

configureMapping - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

configureOptions - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

configureOptions - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

configureParser - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

configureParser - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

configureParser - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

configureParser - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

configurePlugin - Variable in class net.sf.basedb.plugins.Base1PluginExecuter

Holds information about a plugin configuration request.

configurePlugin - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

configurePlugin - Variable in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter

configurePlugin - Variable in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator

configurePlugin - Variable in class net.sf.basedb.plugins.ManualTransformCreator

configurePlugin - Variable in class net.sf.basedb.plugins.PackedFileExporter

configurePlugin - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter

configurePlugin - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

configurePlugin - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

configureQuery(DbControl, EntityQuery, boolean) - Method in class net.sf.basedb.core.ItemContext

configureQuery(DbControl, EntityQuery, ClientContext, boolean) - Method in class net.sf.basedb.core.ItemContext

Use the settings in this context to configure a query.

configureQuery(DbControl, SqlQuery, List<String>) - Method in class net.sf.basedb.core.ItemContext

Use the settings in this context to configure a dynamic query.

configureQuery(SqlQuery) - Method in interface net.sf.basedb.util.DynamicFilter

Configure the query before it is used.

configureQuery(SqlQuery) - Method in class net.sf.basedb.util.IncludeExcludeFilter

We need the position which is in column 2 (already selected).

configureRawDataType - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

configureSelection - Variable in class net.sf.basedb.plugins.PluginConfigurationImporter

connect() - Method in class net.sf.basedb.util.jobagent.JobAgentConnection

Create a socket connection to the job agent.

connection() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

Deprecated.

ConnectionClosedException - Exception in net.sf.basedb.core

This exception is thrown when trying to use a DbControl object that has been closed.

ConnectionClosedException() - Constructor for exception net.sf.basedb.core.ConnectionClosedException

Creates a new ConnectionClosedException.

ConnectionManager - Interface in net.sf.basedb.util.uri

A connection manager is used to access the contents and metadata about the resource pointed to by a given URI.

connectionManagerFactory - Variable in class net.sf.basedb.core.data.FileServerData

ConnectionManagerFactory - Interface in net.sf.basedb.util.uri

A connection manager factory is responsible for creating connection managers for some subset of URI:s that is supported.

ConnectionManagerUtil - Class in net.sf.basedb.util.uri

Collects utility methods related to connection managers.

ConnectionManagerUtil() - Constructor for class net.sf.basedb.util.uri.ConnectionManagerUtil

ConnectionParameters - Class in net.sf.basedb.util.uri

Connection parameters, such as username/password, that may be needed to connect to a server.

ConnectionParameters() - Constructor for class net.sf.basedb.util.uri.ConnectionParameters

Create a new empty parameters object.

connectTimeout - Variable in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager

ConsoleProgressReporter - Class in net.sf.basedb.util

An implementation of the ProgressReporter interface that writes all messages to the standard console.

ConsoleProgressReporter() - Constructor for class net.sf.basedb.util.ConsoleProgressReporter

ConsoleProgressReporter(boolean) - Constructor for class net.sf.basedb.util.ConsoleProgressReporter

constant - Variable in class net.sf.basedb.util.parser.ConstantMapper

ConstantMapper - Class in net.sf.basedb.util.parser

A constant string mapper.

ConstantMapper(Float) - Constructor for class net.sf.basedb.util.parser.ConstantMapper

ConstantMapper(Integer) - Constructor for class net.sf.basedb.util.parser.ConstantMapper

ConstantMapper(String) - Constructor for class net.sf.basedb.util.parser.ConstantMapper

Create a constant mapper.

ConstantMapper(String, NumberFormat, boolean) - Constructor for class net.sf.basedb.util.parser.ConstantMapper

Create a constant mapper using a specific number formatter as it's parser.

ConstantMapper(String, NumberFormat, Formatter<Date>, boolean) - Constructor for class net.sf.basedb.util.parser.ConstantMapper

Create a constant mapper using a specific number formatter as it's parser.

ConstantMapper(Date, Formatter<Date>) - Constructor for class net.sf.basedb.util.parser.ConstantMapper

constructor - Variable in enum class net.sf.basedb.core.Item

contact - Variable in class net.sf.basedb.core.data.PluginDefinitionData

contact - Variable in class net.sf.basedb.core.plugin.AboutImpl

contact - Variable in class net.sf.basedb.util.extensions.AboutBean

contact - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredAbout

contains(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

contains(Object) - Method in class net.sf.basedb.core.ItemResultList

contains(Object) - Method in class net.sf.basedb.util.Tree

contains(String, Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

contains(AnnotationUtil.AnnotatableWrapper) - Method in class net.sf.basedb.util.AnnotationUtil.Cache

containsAll(Collection<?>) - Method in class net.sf.basedb.core.AbstractResultList

containsAll(Collection<?>) - Method in class net.sf.basedb.core.UnmodifiableResultList

containsAll(Collection<?>) - Method in class net.sf.basedb.util.Tree

containsKey(Object) - Method in class net.sf.basedb.util.formatter.LookupFormatter

Checks if a given key has been registered.

containsKey(Object) - Method in class net.sf.basedb.util.jep.FunctionSafeJep.SafeFunctionTable

If the key is already registered, return TRUE.

content - Variable in class net.sf.basedb.clients.web.extensions.section.SectionBean

content - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory

content - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean

content - Variable in class net.sf.basedb.clients.web.taglib.tab.TabControl

The HTML for the contents of the tabs.

ContentSecurityPolicyFilter - Class in net.sf.basedb.clients.web.servlet

This is a filter that sets the "Content-Security-Policy" header in the http response.

ContentSecurityPolicyFilter() - Constructor for class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter

ContentSecurityPolicyReportServlet - Class in net.sf.basedb.clients.web.servlet

This is a servlet for posting reports from "Content-Security-Policy" violations.

ContentSecurityPolicyReportServlet() - Constructor for class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyReportServlet

contentStyle - Variable in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory

contentStyle - Variable in class net.sf.basedb.clients.web.extensions.section.SectionBean

contentStyle - Variable in class net.sf.basedb.clients.web.taglib.HideableSection

Optional style attribute for the content section

contentStyle - Variable in class net.sf.basedb.clients.web.taglib.tab.TabControl

Optional style attribute for the content section

context - Variable in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor

context - Variable in class net.sf.basedb.clients.web.extensions.renderer.PrefixSuffixRenderer

context - Variable in class net.sf.basedb.clients.web.extensions.ServletWrapper

context - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab

context - Variable in class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRenderer

context - Variable in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarButtonRenderer

context - Variable in class net.sf.basedb.clients.web.taglib.extensions.Render

context - Variable in class net.sf.basedb.clients.web.taglib.extensions.Scripts

context - Variable in class net.sf.basedb.clients.web.taglib.extensions.Stylesheets

context - Variable in class net.sf.basedb.clients.web.taglib.HideableSection

context - Variable in class net.sf.basedb.core.PluginConfigurationRequest

context - Variable in class net.sf.basedb.core.signal.ExtensionSignalTransporter

context - Variable in class net.sf.basedb.util.overview.node.NodeFactory

CONTEXT_BIOASSAYS - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

GuiContext = [Item.BIOASSAY, GuiContext.Type.LIST]

CONTEXT_BIOASSAYSET - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

GuiContext = [Item.BIOASSAYSET, GuiContext.Type.ITEM]

CONTEXT_DERIVEDBIOASSAY - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

GuiContext = [Item.DERIVEDBIOASSAY, GuiContext.Type.ITEM]

CONTEXT_RELATIVE - Enum constant in enum class net.sf.basedb.util.extensions.xml.PathType

Paths should be relative to the web application context.

ContextData - Class in net.sf.basedb.core.data

This class holds context information to help client applications with storing common settings for tables.

ContextData() - Constructor for class net.sf.basedb.core.data.ContextData

contextDestroyed(ServletContextEvent) - Method in class net.sf.basedb.clients.web.servlet.StartStopServlet

contextId - Variable in class net.sf.basedb.core.ItemContext

ContextIndex - Class in net.sf.basedb.core.data

ContextIndex() - Constructor for class net.sf.basedb.core.data.ContextIndex

ContextIndex(ClientData, int, String, String) - Constructor for class net.sf.basedb.core.data.ContextIndex

contextInitialized(ServletContextEvent) - Method in class net.sf.basedb.clients.web.servlet.StartStopServlet

contextItem - Variable in class net.sf.basedb.core.data.JobData

ContextKey - Class in net.sf.basedb.core

ContextKey(Item, String) - Constructor for class net.sf.basedb.core.ContextKey

Create a new ContextKey object from Item and it's subcontext.

contextMessage - Variable in class net.sf.basedb.util.ContextUtil.ContextResult

contextPath - Variable in class net.sf.basedb.clients.web.servlet.ImageRemapFilter

contextPath - Variable in class net.sf.basedb.clients.web.servlet.RssNewsFeed

ContextResult(PluginDefinition, PluginConfiguration, String) - Constructor for class net.sf.basedb.util.ContextUtil.ContextResult

Create a new warning-level result object.

ContextResult(PluginDefinition, PluginConfiguration, Throwable) - Constructor for class net.sf.basedb.util.ContextUtil.ContextResult

Create a new error-level result object.

ContextResult(SessionControl, PluginDefinition, PluginConfiguration, GuiContext, Object) - Constructor for class net.sf.basedb.util.ContextUtil.ContextResult

contexts - Variable in class net.sf.basedb.core.data.ClientData

contexts - Variable in class net.sf.basedb.core.data.UserData

contexts - Variable in class net.sf.basedb.util.extensions.ExtensionsInvoker

contextType - Variable in class net.sf.basedb.core.data.GuiContextData

contextType - Variable in class net.sf.basedb.core.data.JobData

ContextUtil - Class in net.sf.basedb.util

A class with utility methods for plug-ins.

ContextUtil() - Constructor for class net.sf.basedb.util.ContextUtil

ContextUtil.ContextResult - Class in net.sf.basedb.util

Class for holding the result of a call to the InteractivePlugin.isInContext(GuiContext, Object) method.

ContextUtil.IsInContextFilter - Class in net.sf.basedb.util

Filter implementation that works on collections of ContextUtil.ContextResult:s and return only those that return true from ContextUtil.ContextResult.isInContext().

CONTINUE - Enum constant in enum class net.sf.basedb.core.plugin.Response.Status

continueAfterError - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

continueLater(String, boolean, Serializable) - Method in class net.sf.basedb.core.Job

This method is used to indicate that a job had to be aborted due to a system shutdown.

continueWithNextFileAfterError(Throwable) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

If the importer should continue with the next file after an error.

continueWithNextFileAfterError(Throwable) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter

We will continue if: The file is not of the correct format, eg. t = UnsupportedFileFormatException.

Controlled - Interface in net.sf.basedb.core

This is the base tagging interface for items that needs special attention by the DbControl object when DbControl.commit() is called.

convert(Enum<T>) - Method in class net.sf.basedb.util.json.EnumConverter

convert(String) - Method in class net.sf.basedb.util.extensions.debug.StringConverter

convert(String, Method) - Method in class net.sf.basedb.util.extensions.xml.PathConverter

convert(String, Method) - Method in interface net.sf.basedb.util.extensions.xml.ValueConverter

Convert a value.

convert(String, Method) - Method in class net.sf.basedb.util.extensions.xml.VariableConverter

convert(T) - Method in class net.sf.basedb.util.json.IdentityConverter

convert(T) - Method in interface net.sf.basedb.util.json.JsonConverter

Convert the given object to a JSON-compatible object.

convert(T) - Method in class net.sf.basedb.util.json.NameableConverter

converter - Variable in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil

converter - Static variable in class net.sf.basedb.util.extensions.debug.StringConverter

ConverterFactory - Class in net.sf.basedb.util.jep.convert

Keep JepConversionFunction objects for converting built-in JEP object to Query API Expression or Restriction objects.

ConverterFactory() - Constructor for class net.sf.basedb.util.jep.convert.ConverterFactory

converters - Variable in class net.sf.basedb.util.extensions.xml.XmlLoader

converters - Static variable in class net.sf.basedb.util.jep.convert.ConverterFactory

convertJavaDateFormatToExcelFormat(String) - Static method in class net.sf.basedb.util.excel.CellStyleCreator

Converts a Java date format string to the corresponding Excel date format string.

convertNumber(Number) - Method in enum class net.sf.basedb.core.Type

Convert a number to the appropriate class.

convertPresets(ProgressReporter) - Static method in class net.sf.basedb.core.Update

Convert presets to use subtype/subcategories if they have filters that are matching existing configuration.

convertString(Class, String) - Static method in class net.sf.basedb.util.extensions.debug.StringConverter

convertSyncFilters(ProgressReporter) - Static method in class net.sf.basedb.core.Update

Convert sync filters to use subtype if they have filters that are matching existing configuration.

convertToNull(String) - Method in class net.sf.basedb.util.parser.FlatFileParser

convertToReferenceUnit(double) - Method in class net.sf.basedb.util.units.IdentityUnitConverter

convertToReferenceUnit(double) - Method in class net.sf.basedb.util.units.LinearUnitConverter

value(ref) = value(specific) * factor + offset

convertToReferenceUnit(double) - Method in interface net.sf.basedb.util.units.UnitConverter

Convert a value from the specific unit to the reference unit.

convertToSpecificUnit(double) - Method in class net.sf.basedb.util.units.IdentityUnitConverter

convertToSpecificUnit(double) - Method in class net.sf.basedb.util.units.LinearUnitConverter

value(specific) = (value(ref) - offset) / factor

convertToSpecificUnit(double) - Method in interface net.sf.basedb.util.units.UnitConverter

Convert a value from the reference unit to the specific unit.

convertValue(String, Class<?>) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory

Convert a string value to another type.

convertValues(AnnotationType, List<?>, Unit) - Method in class net.sf.basedb.core.Annotation

convertValueToUnit(Session, String, String, Unit) - Method in class net.sf.basedb.core.PropertyFilter

Converts a string to a numeric value with the correct unit.

Coordinate - Class in net.sf.basedb.util

Util class for coordinate transformations in base.

Coordinate() - Constructor for class net.sf.basedb.util.Coordinate

COORDINATES - Enum constant in enum class net.sf.basedb.core.FeatureIdentificationMethod

Use coordinates (block, metaGridX, metaGridY, row, column)

coordinateType - Variable in class net.sf.basedb.core.data.DataCubeExtraValueData

CoordinateType(int) - Constructor for enum class net.sf.basedb.core.ExtraValue.CoordinateType

copy(byte[], int, int) - Method in class net.sf.basedb.util.InputStreamSplitter

Write data to all output streams.

copy(int) - Method in class net.sf.basedb.util.InputStreamSplitter

Write data to all output streams.

copy(InputStream, OutputStream) - Static method in class net.sf.basedb.util.FileUtil

Copy from the input stream to the output stream until end of file is reached.

copy(InputStream, OutputStream, AbsoluteProgressReporter) - Static method in class net.sf.basedb.util.FileUtil

Copy from the input stream to the output stream until end of file is reached.

copy(Reader, Writer) - Static method in class net.sf.basedb.util.FileUtil

Copy from the reader to the writer until end of file is reached.

copy(Reader, Writer, AbsoluteProgressReporter) - Static method in class net.sf.basedb.util.FileUtil

Copy from the reader to the writer until end of file is reached.

copy(Date) - Static method in class net.sf.basedb.core.DateUtil

Get a copy of the date.

copy(File, File) - Method in class net.sf.basedb.plugins.Base1PluginExecuter

Copies the content from a File to a directory on the file system.

copy(About, boolean) - Method in class net.sf.basedb.util.extensions.AboutBean

Copy information from antoher About object to this one.

COPY_ANNOTATIONS - Static variable in class net.sf.basedb.core.plugin.AbstractPlugin

The name of the parameter that asks if annotations should be copied or not.

copyFrom(Annotatable, boolean) - Method in class net.sf.basedb.core.AnnotationSet

Copy annotations from another annotatable item to this annotation set.

copyFrom(ItemContext, boolean) - Method in class net.sf.basedb.core.ItemContext

Copy settings from another context to this context.

copyFromSyncFilter(ItemListSyncFilterData) - Method in class net.sf.basedb.core.ItemContext

copyMetadata(FusionCDFData, ArrayDesign) - Method in class net.sf.basedb.util.affymetrix.CdfValidator

Copy metadata from the CDF file to the array design.

copyMetadata(FusionCELData, RawBioAssay) - Method in class net.sf.basedb.util.affymetrix.CelValidator

Copy metadata from the CEL file to the raw bioassay.

copyNotNulls(Collection<? extends T>, T[]) - Static method in class net.sf.basedb.core.query.Restrictions

copyNotNulls(T[], T[]) - Static method in class net.sf.basedb.core.query.Restrictions

copyObjectsAndTemporaryFilters(ItemContext) - Method in class net.sf.basedb.core.ItemContext

Copies all objects and temporary filters from this context to another context.

copyParametersFrom(Job) - Method in class net.sf.basedb.core.Job

Copy all parameter values from another job.

copyParametersFrom(PluginConfiguration) - Method in class net.sf.basedb.core.PluginConfiguration

Copy all parameter values from another plugin configuration.

copyPermissions(DbControl, Shareable, Shareable) - Static method in class net.sf.basedb.core.ShareableUtil

Copy permissions from one item to another.

copyProperties(File, File) - Static method in class net.sf.basedb.util.zip.PackUtil

Copy certain properties from the archive file to the unpacked file.

copyRedefinedColumnNames(BaseFileParser) - Method in class net.sf.basedb.util.basefile.BaseFileParser

Copy redefined column names from the given parser into this parser.

copyReporterFields(int, Object[], int) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

Copy cached reporter data into a data array.

copyright - Variable in class net.sf.basedb.core.data.PluginDefinitionData

copyright - Variable in class net.sf.basedb.core.plugin.AboutImpl

copyright - Variable in class net.sf.basedb.util.extensions.AboutBean

copyright - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredAbout

copySkipped - Variable in class net.sf.basedb.util.InputStreamSplitter

If the InputStreamSplitter.skip(long) method should copy to the output streams or no.

copySubdirectories(DbControl, Directory, Directory, User) - Static method in class net.sf.basedb.core.Directory

This method copies a directory strucure to the destination directory.

copySyncFiltersAndMembers(DbControl, ItemList) - Method in class net.sf.basedb.core.ItemList

Copy all sync filters and list members from the given list.

copyTo - Variable in class net.sf.basedb.util.InputStreamSplitter

Streams to copy the data to.

copyToContext(ItemContext) - Method in class net.sf.basedb.core.SyncFilter

Copy the filter settings in this synchronization filter to the given item context.

copyToStdout - Variable in class net.sf.basedb.util.extensions.logging.ExtensionsLog

copyToSyncFilter(ItemListSyncFilterData) - Method in class net.sf.basedb.core.ItemContext

Create a new item list synchronization filter from this context.

correct(double, double, double) - Method in class net.sf.basedb.util.ma.Log10MACalculator

ch1 = old - factor * log10(2) ch2 = old + factor * log10(2)

correct(double, double, double) - Method in class net.sf.basedb.util.ma.Log2MACalculator

ch1 = old - factor ch2 = old + factor

correct(double, double, double) - Method in class net.sf.basedb.util.ma.MACalculator

Apply a correction factor to the ch1 and ch2 intensity values.

couldParse - Variable in class net.sf.basedb.core.File.CharsetTesterThread

couldParse() - Method in class net.sf.basedb.core.File.CharsetTesterThread

Returns TRUE if the file seems like valid (UTF-8).

count - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup

count - Variable in class net.sf.basedb.core.AnnotationBatcher.UpdateBatcher

count - Variable in class net.sf.basedb.util.AnyToAnyLinkStatistics

count - Variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin

count(Collection<ItemList>, int, int, ItemList.DelayedAdditionManager) - Static method in class net.sf.basedb.core.ItemList

Count the number of times each item is present in the given lists and return those items that are found in >=minCount and <=maxCount lists.

count(Collection<ReporterList>, int, int) - Static method in class net.sf.basedb.core.ReporterList

Count the number of times each reporter is present in the given lists and return those reporters that are found in >=minCount and <=maxCount lists.

count(DbControl) - Method in class net.sf.basedb.core.AbstractEntityQuery

count(DbControl) - Method in class net.sf.basedb.core.AbstractHqlQuery

count(DbControl) - Method in class net.sf.basedb.core.AbstractSqlQuery

count(DbControl) - Method in interface net.sf.basedb.core.query.Query

Count the number of items/rows that are returned by the query.

count(Expression, boolean) - Static method in class net.sf.basedb.core.query.Aggregations

Calculates the number of values for an expression: new expression = COUNT(e)

COUNT - Enum constant in enum class net.sf.basedb.util.plot.HistogramPlot.YAggregate

Plot the number of spots falling into each bin.

countBioAssaySpots() - Method in class net.sf.basedb.core.BioAssaySet

countChildren(boolean) - Method in class net.sf.basedb.core.BioMaterial

Count the number of already existing children to this biomaterial.

countChildren(boolean) - Method in class net.sf.basedb.core.BioSource

Count the number of child samples.

countChildren(boolean) - Method in class net.sf.basedb.core.Extract

Count the number of child extracts.

countChildren(boolean) - Method in class net.sf.basedb.core.Sample

Count the number of child samples or extracts.

counter - Variable in class net.sf.basedb.clients.web.plugins.DynamicQueryWrapper

CountExpression - Class in net.sf.basedb.core.query

Count the number of values: COUNT(e)

CountExpression(Expression, boolean) - Constructor for class net.sf.basedb.core.query.CountExpression

countExtracts() - Method in class net.sf.basedb.core.Extract

Counts all extracts that have been created from this extract.

countExtracts() - Method in class net.sf.basedb.core.Sample

Counts all extracts that have been created from this sample.

countNotNulls(Object[]) - Static method in class net.sf.basedb.core.query.Restrictions

countNotNulls(Collection<?>) - Static method in class net.sf.basedb.core.query.Restrictions

countPlugins(DbControl, GuiContext) - Static method in class net.sf.basedb.core.PluginDefinition

Count the number of plugins that can be used in a given context.

countProjectSpecificAnnotations() - Method in class net.sf.basedb.core.AnnotationType

Count the number of project-specific annotations that exists for this annotation type.

countQuery - Variable in class net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter

countQuery - Variable in class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter

countRawBioAssays() - Method in class net.sf.basedb.core.DerivedBioAssay

Counts all raw bioassays that have been created from this bioassay.

countRootDerivedBioAssays() - Method in class net.sf.basedb.core.PhysicalBioAssay

Counts all root derived bioassays that have been created from this physical bioassay.

country - Variable in class net.sf.basedb.util.GeoLocation

countSamples() - Method in class net.sf.basedb.core.BioSource

Counts all samples that have been created from this biosource.

countSamples() - Method in class net.sf.basedb.core.Sample

Counts all samples that have been created from this sample.

countSpotMappings() - Method in class net.sf.basedb.core.DataCube

Count the number of raw data mappings for the spot with the most mappings.

countSpotsAndReporters() - Method in class net.sf.basedb.core.BioAssaySet

Count the number of unique reporters and spots in all bioassays in this bioassayset.

countUnreadMessages(DbControl, User, boolean) - Static method in class net.sf.basedb.core.Message

Count the number of unread messages for the specified or logged in user.

countUsuablePlugins(Collection<ContextUtil.ContextResult>) - Static method in class net.sf.basedb.util.ContextUtil

Count all plug-in / configuration combinations that can be used.

CountWork(SessionControl, String, List<String>) - Constructor for class net.sf.basedb.core.AbstractSqlQuery.CountWork

cpuUsage - Variable in class net.sf.basedb.util.jobagent.JobAgentInfo

create(File) - Static method in class net.sf.basedb.util.bfs.AnnotationParser

Utility method for creating an annotation parser for a file in the local file system.

create(File) - Static method in class net.sf.basedb.util.bfs.AnnotationWriter

Utility method for creating an annotation writer to a file in the native file system.

create(File) - Static method in class net.sf.basedb.util.bfs.DataParser

Utility method for creating a data parser for a file in the local file system.

create(File) - Static method in class net.sf.basedb.util.bfs.DataWriter

Utility method for creating a data writer to a file in the native file system.

create(File) - Static method in class net.sf.basedb.util.bfs.MetadataParser

Utility method for creating a metadata parser for a file in the local file system.

create(File) - Static method in class net.sf.basedb.util.bfs.MetadataWriter

Utility method for creating a metadata writer to a file in the native file system.

create(InputStream, String, long) - Static method in class net.sf.basedb.util.bfs.AnnotationParser

Utility method for creating an annotation parser when you have an input stream.

create(InputStream, String, long) - Static method in class net.sf.basedb.util.bfs.DataParser

Utility method for creating a data parser when you have an input stream.

create(InputStream, String, long) - Static method in class net.sf.basedb.util.bfs.MetadataParser

Utility method for creating a metadata parser when you have an input stream.

create(OutputStream, String) - Static method in class net.sf.basedb.util.bfs.AnnotationWriter

Utility method for creating an annotation writer when you have an output stream.

create(OutputStream, String) - Static method in class net.sf.basedb.util.bfs.DataWriter

Utility method for creating a data writer when you have an output stream.

create(OutputStream, String) - Static method in class net.sf.basedb.util.bfs.MetadataWriter

Utility method for creating a metadata writer when you have an output stream.

create(Class<?>) - Static method in class net.sf.basedb.core.log.EntityLogOptions

create(String) - Static method in class net.sf.basedb.core.ClonableProperty

Create a cloned property from either an extended or static property.

create(String, PropertyFilterData) - Static method in class net.sf.basedb.core.PropertyFilter

Create a property filter instance from what has been saved in the database.

create(String, Item, String) - Static method in class net.sf.basedb.clients.web.plugins.AnyToAnyDataLoader

Create a new data loader that load a value from an any-to-any link.

create(ResultSet, int, Writer, TableInfo.ColumnInfo) - Method in class net.sf.basedb.core.migrate.postgres.PostgresResultWriterFactory

create(ResultSet, int, Writer, TableInfo.ColumnInfo) - Method in interface net.sf.basedb.core.migrate.ResultWriterFactory

Create a new result writer.

create(FileServerData) - Static method in class net.sf.basedb.util.uri.ConnectionParameters

Create a parameters object using information from the FileServer object.

create(DbControl, int, RelatedItemColumn.Specification, RelatedItemHelper) - Static method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn

For now, we assume that 'expr' is one of: /DIRECTION/ITEMTYPE/subtype-id/#annotationtype-id /DIRECTION/ITEMTYPE/subtype-id/!

create(DbControl, int, Item, String, FileViewerUtil) - Static method in class net.sf.basedb.clients.web.extensions.list.AnyLinkColumn

For now, we assume that 'expr' is |linkName|ITEMTYPE|property ITEMTYPE and property are optional.

create(File) - Static method in class net.sf.basedb.util.bfs.AnnotationParser

Utility method for creating an annotation parser for a file in the BASE file system.

create(File) - Static method in class net.sf.basedb.util.bfs.AnnotationWriter

Utility method for creating an annotation writer to a file in the BASE file system.

create(File) - Static method in class net.sf.basedb.util.bfs.DataParser

Utility method for creating a data parser for a file in the BASE file system.

create(File) - Static method in class net.sf.basedb.util.bfs.DataWriter

Utility method for creating a data writer to a file in the BASE file system.

create(File) - Static method in class net.sf.basedb.util.bfs.MetadataParser

Utility method for creating a metadata parser for a file in the BASE file system.

create(File) - Static method in class net.sf.basedb.util.bfs.MetadataWriter

Utility method for creating a metadata writer to a file in the BASE file system.

create(Item, SyncFilter.SourceItemTransform) - Method in interface net.sf.basedb.util.listable.SourceItemTransformerFactory

Create a source item transformed that can transform between the given source item and the SourceItemTransformerFactory.getTargetItem().

create(Item, SyncFilter.SourceItemTransform) - Method in class net.sf.basedb.util.listable.SourceItemTransformerWithCache

create(Item, SyncFilter.SourceItemTransform) - Method in class net.sf.basedb.util.listable.ToBioSourceSourceItemTransformerFactory

create(Item, SyncFilter.SourceItemTransform) - Method in class net.sf.basedb.util.listable.ToDerivedBioAssaySourceItemTransformerFactory

create(Item, SyncFilter.SourceItemTransform) - Method in class net.sf.basedb.util.listable.ToExtractSourceItemTransformerFactory

create(Item, SyncFilter.SourceItemTransform) - Method in class net.sf.basedb.util.listable.ToPhysicalBioAssaySourceItemTransformerFactory

create(Item, SyncFilter.SourceItemTransform) - Method in class net.sf.basedb.util.listable.ToRawBioAssaySourceItemTransformerFactory

create(Item, SyncFilter.SourceItemTransform) - Method in class net.sf.basedb.util.listable.ToSampleSourceItemTransformerFactory

create(Mapper) - Static method in class net.sf.basedb.plugins.batchimport.UsedQuantityMapper

CREATE - Enum constant in enum class net.sf.basedb.core.log.ChangeType

CREATE - Enum constant in enum class net.sf.basedb.core.Permission

This permission allows a user create new items.

CREATE - Enum constant in enum class net.sf.basedb.core.Transactional.Action

The item is a new item and is beeing saved to the database for the first time.

CREATE_BIOMATERIAL - Static variable in class net.sf.basedb.core.BioPlateEventType

The system ID for "Create" event type.

createAgent(Properties) - Method in class net.sf.basedb.clients.jobagent.AgentController

createAllCopy(String) - Static method in class net.sf.basedb.core.ReporterCloneTemplate

createAnnotationType(String, String, Type, int, Object[], Item[], Map<String, String>, boolean, boolean, UserData, ItemKeyData) - Static method in class net.sf.basedb.core.Install

Create an AnnotationType.

createBean(Class<? extends Action>) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory

Create the bean instance.

createBioPlateEventType(String, String, String) - Static method in class net.sf.basedb.core.Install

Create a BioPlateEventType.

createBioPlateType(String, String, Item, ItemSubtypeData, BioWell.LockMode) - Static method in class net.sf.basedb.core.Install

Create a BioPlateType.

createBlockHeaders(List<String>, ArrayDesign, Integer, List<ArrayDesignBlock>) - Method in class net.sf.basedb.plugins.GalExporter

Create header entries for each block in the array design.

createCache() - Static method in class net.sf.basedb.util.AnnotationUtil

Create a new cache object that can be used with AnnotationUtil.getAllAnnotatableParentItems(DbControl, Annotatable, Filter, Cache)

createChildBioAssays(DbControl, BioAssaySet, BaseFileInfo, boolean) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter

Helper method for creating new child bioassays using the information found in the BaseFileInfo object.

createChildBioAssaySet(DbControl, BaseFileInfo, Transformation, boolean) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter

Helper method for creating a child bioassay set using the information in the BaseFileInfo object.

createChildNodes(DbControl, OverviewContext, Node) - Method in interface net.sf.basedb.util.overview.extensions.ChildNodeLoaderAction

Create child nodes for the given parent node.

createChildPositionReporterMapping(BioAssaySet, BaseFileInfo, ProgressReporter) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter

Helper method for creating position/reporter mappings for the child bioassay set (which must be in a new datacube).

createChildRawDataMapping(BioAssaySet, BioAssaySet, BaseFileInfo, ProgressReporter) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter

Helper method for creating a rawdata mapping for the child bioassay set.

createClient(UserData, String, String, String, ItemKeyData) - Static method in class net.sf.basedb.core.Install

Create a Client.

createCloseableHttpClient(URI, ConnectionParameters) - Method in class net.sf.basedb.util.uri.http.HttpConnectionManager

Get a HttpClient object that has been configured to access the given URI.

createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Create mappers that can be used to extract data values from the file that is currently being parsed by the ffp FlatFileParser.

createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter

createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter

createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.ArraySlideImporter

createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.BioPlateImporter

createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.BioSourceImporter

createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.ExtractImporter

createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.FileImporter

createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.KitImporter

createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter

createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.SampleImporter

createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.TagImporter

createConnectionManager(URI, ConnectionParameters) - Method in interface net.sf.basedb.util.uri.ConnectionManagerFactory

Create a new handler for accessing the resource at the given URI.

createConnectionManager(URI, ConnectionParameters) - Static method in class net.sf.basedb.util.uri.ConnectionManagerUtil

Utility method for creating a connection manager.

createConnectionManager(URI, ConnectionParameters) - Method in class net.sf.basedb.util.uri.http.HttpConnectionManagerFactory

createConnectionManager(File, ConnectionParameters) - Static method in class net.sf.basedb.util.uri.ConnectionManagerUtil

Utility method for creating a connection manager for a file item.

createContext(DbControl, PageContext) - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Create a new JspContext object with an active DbControl.

createContext(DbControl, PageContext, GuiContext, Object) - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Deprecated.

In 3.20, use ExtensionsControl.createContext(DbControl, ItemContext, PageContext, GuiContext, Object) instead

createContext(DbControl, ItemContext, PageContext, GuiContext, Object) - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Create a new JspContext object with an active DbControl and a current GuiContext and item.

createContext(SessionControl, PageContext) - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Create a new JspContext object without an active DbControl.

createCountWork(DbControl) - Method in class net.sf.basedb.core.AbstractSqlQuery

Creates a work item for counting the number of total hits by the query.

createCriteria(Class) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

Deprecated.

createCriteria(Class) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

Deprecated.

createCriteria(Class, String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

Deprecated.

createCriteria(Class, String) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

Deprecated.

createCriteria(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

Deprecated.

createCriteria(String) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

Deprecated.

createCriteria(String, String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

Deprecated.

createCriteria(String, String) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

Deprecated.

created - Variable in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlot

created - Variable in class net.sf.basedb.core.data.JobData

created - Variable in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot

created - Variable in class net.sf.basedb.util.jobagent.JobAgentInfo

createDataFileType(String, String, String, Item, String, ItemSubtypeData, Install.ItemSubtypeFT...) - Static method in class net.sf.basedb.core.Install

Create a DataFileType.

createDataWriter(Object, String) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter

Utility method for calling creating a data writer.

createDataWriter(T, String) - Method in class net.sf.basedb.util.bfs.AbstractDataWriterFactory

createDataWriter(T, String) - Method in interface net.sf.basedb.util.bfs.DataWriterFactory

Create a data writer for writing data that belongs to the given owner.

createDataWriters() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter

Create the exact number of data writers that is needed to export the desired data.

createDataWriters() - Method in class net.sf.basedb.util.export.spotdata.MatrixBfsExporter

Create one data writer for each registered spot field.

createDataWriters() - Method in class net.sf.basedb.util.export.spotdata.SerialBfsExporter

Create one data writer for each assay in the bioassay set.

createdColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.SampleImporter

Column mapping parameter for the sample creation date.

createDefaultContext(String, String) - Static method in class net.sf.basedb.clients.web.Base

Create a default context where the sortProperty is also used as the default sticky column.

createDefaultContext(String, String, String) - Static method in class net.sf.basedb.clients.web.Base

Create a default ItemContext with settings for default visible columns and sort property.

createDelayedAdditionManager() - Method in class net.sf.basedb.core.ItemList

createDeniedNode(Node) - Method in class net.sf.basedb.util.overview.node.NodeFactory

Create a node representing an item that the logged in user is denied to access.

createDerivedBioAssay(AnnotationBatcher.InsertBatcher) - Method in class net.sf.basedb.core.MigrateRbaToDba.Rba

Create the new derived bioassay.

createdInherited - Variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager

createDirectory(UserData, DirectoryData, String, String, String, ItemKeyData, boolean) - Static method in class net.sf.basedb.core.Install

Create a Directory.

createdMapper - Variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter

createdMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter

createdMapper - Variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter

createdMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter

createDom(String, String) - Static method in class net.sf.basedb.util.XmlUtil2

Create a new Document with root element and System id declaration.

createdPrimary - Variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager

createEngine(Dialect) - Static method in class net.sf.basedb.core.dbengine.EngineFactory

Create a new DbEngine object.

createEntityGraph(Class<T>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

createEntityGraph(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

createExportedProperty(String, String, Metadata, Formatter, ExcelFormatter) - Static method in class net.sf.basedb.clients.web.plugins.ExportedProperty

createFactory(Element, ClassLoader, Class<F>, Presets.Preset) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader

Create a new factory instance.

createFailure(OverviewContext, Set<String>, Validator, Node, String) - Method in class net.sf.basedb.util.overview.validator.NameableNodeValidator

Create a failure on this node unless we have created a failure for the same validator already.

createFailure(Validator, Node, String, Fix...) - Method in class net.sf.basedb.util.overview.GenericOverview

Register a failure of a validation rule.

createFailure(Validator, Node, String, Fix...) - Method in interface net.sf.basedb.util.overview.OverviewContext

Register the failure of a validation rule.

createFile(File, String) - Method in class net.sf.basedb.plugins.BfsExporterPlugin

createFile(String) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

Create a new file in the working directory.

createFile(DbControl, Directory, String) - Method in class net.sf.basedb.plugins.BfsExporterPlugin

createFilter(Object, String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

Deprecated.

createFilteredBioAssaySet(DbControl, BioAssaySet, List<BioAssay>, Job, Restriction, ProgressReporter) - Static method in class net.sf.basedb.util.BioAssaySetFilterUtil

Create a filtered bioassay set from a parent bioassay set using a simple restriction.

createFilteredBioAssaySet(DbControl, BioAssaySet, List<BioAssay>, Job, DynamicFilter, ProgressReporter) - Static method in class net.sf.basedb.util.BioAssaySetFilterUtil

createFlatFileParser(InputStream) - Method in class net.sf.basedb.util.bfs.AnnotationParser

Create a new flat file parser that can parse BFS annotation files.

createFlatFileParser(InputStream) - Method in class net.sf.basedb.util.bfs.DataParser

Create a new flat file parser that can parse BFS annotation files.

createFlatFileParser(InputStream) - Method in class net.sf.basedb.util.bfs.MetadataParser

Create a new flat file parser that can parse BFS metadata files.

createFont() - Method in class net.sf.basedb.util.excel.CellStyleCreator

Create a new font style.

createFormula(Formula.Type, Type, Formula.Parser, Formula.AverageMethod, IntensityTransform, IntensityTransform, String, String, String, int, String[], ColoringData, UserData, ItemKeyData) - Static method in class net.sf.basedb.core.Install

Create a Formula.

createForwardNode(ArraySlide, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.PhysicalBioAssayLoader

Create a forward-loading bioassay node from an array slide.

createForwardNode(BioPlate, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioWellLoader

Create all-loading biomaterial nodes for each non-empty well on the bioplate.

createForwardNode(BioSource, DbControl, OverviewContext, Node, boolean) - Method in class net.sf.basedb.util.overview.loader.SampleLoader

Create forward-loading sample nodes for the samples that has a given biosource as their parent.

createForwardNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AbstractNodeLoader

createForwardNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArrayBatchLoader

Create forward-loading array batch nodes from a given array design node.

createForwardNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArraySlideLoader

Create forward-loading array slide nodes from a given array batch node.

createForwardNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AutoChildNodeLoader

Call the same method on the 'parent' node loader.

createForwardNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioPlateEventLoader

Create a forward-loading node from a bioplate.

createForwardNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioSourceLoader

Create forward-loading biosource nodes from a biomaterial list for the member biosources.

createForwardNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioWellLoader

Create forward-loading biomaterial nodes from a given bioplate The biomaterial nodes are created directly as child nodes to the bioplate.

createForwardNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader

Create forward-loading bioassay nodes from a given physical bioassay node or a parent derived bioassay set node.

createForwardNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExperimentLoader

Create property-loading experiment nodes from a given rawbioassay node.

createForwardNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtensionChildNodeLoader

Call the same method on the 'parent' node loader.

createForwardNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader

Create forward-loading extract nodes from a given parent sample or extract.

createForwardNode(DbControl, OverviewContext, Node) - Method in interface net.sf.basedb.util.overview.loader.NodeLoader

Create a forward-loading (from parent to child) node for the given parent node.

createForwardNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.NullNodeLoader

createForwardNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.PhysicalBioAssayLoader

Create forward-loading physical bioassay nodes from either an extract or an array slide node.

createForwardNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.RawBioAssayLoader

Create forward-loading raw bioassay nodes from a given parent derived bioassay or extract node.

createForwardNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.SampleLoader

Create forward-loading sample nodes from a given parent biosource or sample.

createForwardNode(DerivedBioAssay, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader

Create forward-loading derived bioassay set nodes that have the given derived bioassay set as the parent

createForwardNode(DerivedBioAssay, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.RawBioAssayLoader

createForwardNode(Extract, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader

createForwardNode(Extract, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.RawBioAssayLoader

createForwardNode(Extract, DbControl, OverviewContext, Node, boolean) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader

Create forward-loading extract nodes for the (pooled) extract that has a given extract among their parents.

createForwardNode(Extract, DbControl, OverviewContext, Node, boolean) - Method in class net.sf.basedb.util.overview.loader.PhysicalBioAssayLoader

Create forward-loading bioassay nodes for the bioassays that has a given extract as a source.

createForwardNode(PhysicalBioAssay, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader

Create forward-loading derived bioassay nodes that have the given physical bioassay as the immediate parent (eg. root bioassays).

createForwardNode(Sample, DbControl, OverviewContext, Node, boolean) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader

Create forward-loading extract nodes for the extracts that has a given sample as their parent.

createForwardNode(Sample, DbControl, OverviewContext, Node, boolean) - Method in class net.sf.basedb.util.overview.loader.SampleLoader

Create forward-loading sample nodes for the (pooled) samples that has a given sample as their parent.

createFromExtended(String) - Static method in class net.sf.basedb.core.ClonableProperty

Create a cloned property representation of an extended property.

createFromRegular(String) - Static method in class net.sf.basedb.core.ClonableProperty

Create a cloned property that represents the "static" property with the given name.

createGenericFilter(String, String, Element) - Method in class net.sf.basedb.core.HibernateUtil.FilterConfigurator

Generic filters can be added as <filter< elements in the mapping file.

createGroup(String, String, boolean, boolean, String) - Static method in class net.sf.basedb.core.Install

Create a Group.

createHardware(String, String, String, ItemSubtypeData, UserData, ItemKeyData) - Static method in class net.sf.basedb.core.Install

Create a HardwareData.

createHeader(String, Object) - Method in class net.sf.basedb.plugins.GalExporter

Create a properly formatted GAL header.

createHistory() - Method in class net.sf.basedb.core.log.db.DbLogManager

createHomeDirectory(DbControl, User, boolean) - Static method in class net.sf.basedb.core.Directory

Creates a homedirectory for a specified user.

createHqlQuery(String, Class<R>) - Method in class net.sf.basedb.core.LogControl

Creates a Hibernate HQL query with a known return type.

createIndex(Session, boolean, String, String, String...) - Static method in class net.sf.basedb.core.Update

createInsertBatcher(Connection, String, int...) - Method in class net.sf.basedb.core.AnnotationBatcher

createInsertBatcher(Connection, String, int...) - Method in class net.sf.basedb.core.MigrateRbaToDba

createInstance(DbControl, PluginDefinition, String, boolean) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

Create and initialize a plug-in instance for the given plug-in definition.

createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Create a new item and populate it with data from the current line.

createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter

createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter

createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.ArraySlideImporter

createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.BioPlateImporter

createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.BioSourceImporter

createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.ExtractImporter

createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.FileImporter

createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.KitImporter

createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter

createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.SampleImporter

createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.TagImporter

createItemKey(String, Map<UserData, Integer>, Map<GroupData, Integer>) - Static method in class net.sf.basedb.core.Install

Create an ItemKey.

createItemNode(NodeFactory<? super S>, S, Object, boolean, Node, ChildNodeDirection) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader

Create a new item node using the supplied node factory.

createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Create a new query that returns items of the importable type.

createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

Calls AnnotationType.getQuery(Item).

createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter

Calls ArrayBatch.getQuery().

createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter

Calls PhysicalBioAssay.getQuery().

createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.ArraySlideImporter

Calls ArraySlide.getQuery().

createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.BioPlateImporter

Calls BioPlate.getQuery().

createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.BioSourceImporter

Calls BioSource.getQuery().

createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

Calls DerivedBioAssay.getQuery().

createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.ExtractImporter

Calls Extract.getQuery().

createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.FileImporter

Calls File.getQuery().

createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.KitImporter

Calls Kit.getQuery().

createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter

Calls PhysicalBioAssay.getQuery().

createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

Calls RawBioAssay.getQuery().

createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.SampleImporter

Calls Sample.getQuery().

createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.TagImporter

Calls Tag.getQuery().

createItemQuery(ItemList) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Create a new query that returns items that are members of the given list.

createItemSpecificFilter(String, Item, String, Element) - Method in class net.sf.basedb.core.HibernateUtil.FilterConfigurator

Item-specific filters are stored internally and registered later by HibernateUtil.FilterConfigurator.registerDelayedFilters(org.hibernate.boot.Metadata).

createItemSpecificFilterDef(String, Item, Element) - Method in class net.sf.basedb.core.HibernateUtil.FilterConfigurator

Clone the <filter-def> with the given name and insert a new item-specific <filter-def> definition into the document given by the <class> element.

createItemSubtype(Item, String, String, String, ItemSubtypeData...) - Static method in class net.sf.basedb.core.Install

Create an ItemSubtype.

createJepExpression(DbControl, String, DynamicQuery) - Static method in class net.sf.basedb.util.BioAssaySetUtil

Parse a JEP expression and create a restrictions that is suitable to be used in a dynamic query.

createJepExpressions(DbControl, RawDataType, String[]) - Static method in class net.sf.basedb.util.IntensityCalculatorUtil

createJepIntensityCalculator(DbControl, RawDataType, String...) - Static method in class net.sf.basedb.util.IntensityCalculatorUtil

Create an intensity calculator from mathematical expressions in strings.

createJepRestriction(DbControl, String, DynamicQuery) - Static method in class net.sf.basedb.util.BioAssaySetUtil

Parse a JEP expression and create a restrictions that is suitable to be used in a dynamic query.

createJobExecutor() - Method in class net.sf.basedb.clients.jobagent.Agent

Create a job executor and initialise it.

createJobQueueChecker() - Method in class net.sf.basedb.clients.jobagent.Agent

Create a job queue checker. and register it with the BASE core scheduler.

createJSON(JSONObject, DbControl, Annotation, Formatter<Object>, boolean) - Static method in class net.sf.basedb.clients.web.AnnotationUtil

createJsonForAnnotationTypeAndAnnotation(DbControl, AnnotationType, Annotation, Annotation, boolean, Set<AnnotationTypeCategory>) - Static method in class net.sf.basedb.clients.web.AnnotationUtil

createKeyManagers(KeyStore, String, String, String) - Static method in class net.sf.basedb.util.ssl.SSLUtil2

createKeyStore(InputStream, String, String, String) - Static method in class net.sf.basedb.util.ssl.SSLUtil2

Create a key-store from the given input stream

createLockedCopy() - Method in class net.sf.basedb.core.ReporterCloneTemplate

Create a deep clone of this template.

createLogFile(String) - Method in class net.sf.basedb.core.plugin.AbstractPlugin

Create a log file in the BASE file system for logging detailed information from a plug-in.

createLoggableString(LogControl, Item, int) - Method in class net.sf.basedb.core.log.db.AnyToAnyLogger

createLogger() - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog

Create a logger that adds messages to this log.

createLogger(String) - Static method in class net.sf.basedb.util.extensions.logging.ExtensionsLog

Create a logger that can add entries to the log for the given extension.

createLoginInfo(Session, UserData, String, boolean, AuthenticationMethod, int) - Method in class net.sf.basedb.core.SessionControl

Create a LoginInfo object and load all information that it needs.

createMappers(RawDataType, FlatFileParser) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter.BatchAndMapHolder

createMetadata(URI, HttpResponse) - Method in class net.sf.basedb.util.uri.http.HttpConnectionManager

Read metadata from the given http response and put the information in a UriMetadata object.

createMimeType(String, String, String, ItemSubtypeData, boolean) - Static method in class net.sf.basedb.core.Install

Create a MimeType.

createMissing - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

createMissingNode(Node) - Method in class net.sf.basedb.util.overview.node.NodeFactory

Create a node representing a missing item.

createMode - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

createMode - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

createNamedQuery(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

createNamedQuery(String) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

createNamedQuery(String, Class<R>) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

createNamedQuery(String, Class<T>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

createNamedStoredProcedureQuery(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

createNativeQuery(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

createNativeQuery(String) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

createNativeQuery(String, Class) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

createNativeQuery(String, Class<R>) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

createNativeQuery(String, String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

createNativeQuery(String, String) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

createNews(String, String) - Static method in class net.sf.basedb.core.Install

Create a News.

createNode(I, Object, Node, ChildNodeDirection) - Method in class net.sf.basedb.util.overview.node.NodeFactory

Create a node representing an existing item.

createNode(I, String, String, Object, Node, ChildNodeDirection) - Method in class net.sf.basedb.util.overview.node.NodeFactory

createNodeLoader(Object) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory

Create a new node loader for loading nodes for the specified item type.

createNodeLoader(K) - Method in interface net.sf.basedb.util.overview.loader.NodeLoaderFactory

Create a node loader that knows how to load nodes for items that are specified by the given key.

createNodeValidator(Object) - Method in class net.sf.basedb.util.overview.validator.BasicItemNodeValidatorFactory

Create a new node validator that can validate nodes with items of the specified item type.

createNodeValidator(K) - Method in interface net.sf.basedb.util.overview.validator.NodeValidatorFactory

Create a node validator that knows how to validate nodes for items that are specified by the given key.

createNotFoundItems - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

createParameterMap() - Method in class net.sf.basedb.core.RequestInformation

Create a hash from parameter name to PluginParameter objects so that the RequestInformation.getParameter(String) method doesn't have to look in the list.

createPermissions - Variable in class net.sf.basedb.core.Job.SignalKeyring

createPlateGeometry(String, String, int, int) - Static method in class net.sf.basedb.core.Install

Create a PlateGeometry.

createPlateMapping(String, String, PlateGeometryData, int, PlateGeometryData, int, String, UserData, ItemKeyData) - Static method in class net.sf.basedb.core.Install

Create a PlateMapping.

createPlatform(String, String, String, boolean, String, int, Install.PlatformFT...) - Static method in class net.sf.basedb.core.Install

Create a Platform.

createPlatformVariant(PlatformData, String, String, String, boolean, String, int, Install.PlatformFT...) - Static method in class net.sf.basedb.core.Install

Create a PlatformVariant.

createPluginConfigurations(String, boolean) - Static method in class net.sf.basedb.core.Install

Create PluginConfigurations from a XML file.

createPluginDefinition(PluginInfo, ItemKey) - Static method in class net.sf.basedb.core.Install

Create a PluginDefinition.

createPluginDefinitions(String, ItemKey, boolean) - Static method in class net.sf.basedb.core.Install

Read plug-in definitions from the given file.

createPluginType(String, String, String, String) - Static method in class net.sf.basedb.core.Install

Create a PluginType.

createPooledReverseNode(Extract, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader

Create reverse-loading extract nodes of a pooled extract.

createPooledReverseNode(Sample, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.SampleLoader

Create reverse-loading samples nodes of a sample with other sample(s) as parent items.

createPropertyElement(ExtendedProperty, Namespace) - Static method in class net.sf.basedb.core.HibernateUtil

Creates a <property> tag from an extended property definition.

createPropertyNode(BioPlateEvent, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioPlateLoader

Create a property node(s) when the parent item is a bioplate event.

createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AbstractNodeLoader

createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AnnotationLoader

createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AnyToAnyLoader

createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArrayDesignLoader

Create an array design property node from a raw bioassay or root raw bioassay node.

createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AutoChildNodeLoader

Call the same method on the 'parent' node loader.

createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioPlateLoader

Create a bioplate property node from a biomaterial that is located on a plate or property nodes for each bioplate that is part of a bioplate event.

createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.DataFileLoader

createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExperimentalFactorLoader

createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtensionChildNodeLoader

Call the same method on the 'parent' node loader.

createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader

A property node is created when moving in the reverse direction so that we can load child extracts+physical bioassays with the ItemSubtype.getPushAnnotations() flag set.

createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.FileLoader

createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.HardwareLoader

createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.KitLoader

createPropertyNode(DbControl, OverviewContext, Node) - Method in interface net.sf.basedb.util.overview.loader.NodeLoader

Create a property node for the given parent node.

createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.NullNodeLoader

createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.PhysicalBioAssayLoader

A property node is created when moving in the reverse direction so that we can load child physical bioassays with the ItemSubtype.getPushAnnotations() flag set.

createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.PlatformLoader

createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ProtocolLoader

createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ProtocolParameterLoader

createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.SampleLoader

A property node is created when moving in the reverse direction so that we can load child samples+extracts with the ItemSubtype.getPushAnnotations() flag set.

createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.SoftwareLoader

createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.TagLoader

createPropertyNode(MeasuredBioMaterial, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioPlateLoader

Create a property node when the parent item is a biomaterial.

createQuantity(String, String, String, String) - Static method in class net.sf.basedb.core.Install

Create a Quantity.

createQuery(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

If the same query has been executed before, return the cached instance, otherwise create a new query from the parent session and cache it.

createQuery(String) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

If the same query has been executed before, return the cached instance, otherwise create a new query from the parent session and cache it.

createQuery(String, Class<R>) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

createQuery(String, Class<T>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

createQuery(CriteriaDelete) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

createQuery(CriteriaDelete) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

createQuery(CriteriaQuery<T>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

createQuery(CriteriaQuery<T>) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

createQuery(CriteriaUpdate) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

createQuery(CriteriaUpdate) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

createQuery(Item, ItemList) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter

Create a query that return items of the specified type.

createQuery(Item, ItemList) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

Create a query that return items of the specified type.

createQuery(Session, String) - Static method in class net.sf.basedb.core.HibernateUtil

Create a Hibernate query.

createQuery(Session, String, Class<R>) - Static method in class net.sf.basedb.core.HibernateUtil

Create a Hibernate query with a known return type.

createQuery(StatelessSession, String, Class<R>) - Static method in class net.sf.basedb.core.HibernateUtil

Create a Hibernate query using a stateless session and a known return type.

createQuota(String, String, String, long) - Static method in class net.sf.basedb.core.Install

Create a Quota.

createQuotaType(String, String, String) - Static method in class net.sf.basedb.core.Install

Create a QuotaType.

createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AbstractNodeLoader

createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArrayBatchLoader

Create a reverse-loading array batch node from an array slide node.

createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArrayDesignLoader

Create a reverse-loading array design node from an array batch node.

createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArraySlideLoader

Create a reverse-loading array slide node from the hyrbidization node.

createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AutoChildNodeLoader

Call the same method on the 'parent' node loader.

createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioSourceLoader

Create a reverse-loading biosource node from a sample node.

createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader

Create a reverse-loading bioassay node from a cild bioassay node or a raw bioassay node.

createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtensionChildNodeLoader

Call the same method on the 'parent' node loader.

createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader

The parent node can be one of: Physical bioassay: Load the source extract(s) and return a folder-type node Extract: Load the parent extracts and return either a folder-type or item-type node depending on the number of parents Raw bioassay: Load the parent extract and return an item-type node Derived bioassay: Load the parent extract and return an item-type node

createReverseNode(DbControl, OverviewContext, Node) - Method in interface net.sf.basedb.util.overview.loader.NodeLoader

Create a reverse-loading (from child to parent) node for the given child node.

createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.NullNodeLoader

createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.PhysicalBioAssayLoader

Create a reverse-loading bioassay node from the derived bioassay node.

createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.RawBioAssayLoader

Create a reverse-loading raw bioassay nodes from a given experiment node.

createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.RootRawBioAssayLoader

Create a reverse-loading raw bioassay nodes from a given experiment node.

createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.SampleLoader

Create reverse-loading sample nodes from an extract node or from a pooled sample.

createReverseNode(DerivedBioAssay, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader

Create a reverse-loading bioassay node for the bioassay that is the parent to the given child bioassay.

createReverseNode(DerivedBioAssay, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader

createReverseNode(PhysicalBioAssay, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader

Create reverse-loading extract nodes from a physical bioassay.

createReverseNode(RawBioAssay, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader

Create a reverse-loading bioassay node for the bioassay that is the parent to the given raw bioassay.

createReverseNode(RawBioAssay, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader

createRole(String, String, boolean, String) - Static method in class net.sf.basedb.core.Install

Create a Role.

createRoleKey(Item, String, String, Map<RoleData, Integer>) - Static method in class net.sf.basedb.core.Install

Create a RoleKey.

createRootBioAssaySet(DbControl, Experiment, Collection<RawBioAssay>, Job, Expression[], ProgressReporter) - Static method in class net.sf.basedb.util.IntensityCalculatorUtil

Create a root bioassayset for a given experiment and set of raw bioassays.

createRootBioAssaySet(DbControl, Experiment, Collection<RawBioAssay>, Job, IntensityCalculator, ProgressReporter) - Static method in class net.sf.basedb.util.IntensityCalculatorUtil

Create a root bioassayset for a given experiment and set of raw bioassays.

createRootNode(DbControl, BasicItem) - Method in class net.sf.basedb.util.overview.GenericOverview

createRootNode(DbControl, OverviewContext, I) - Method in class net.sf.basedb.util.overview.loader.AbstractNodeLoader

createRootNode(DbControl, OverviewContext, I) - Method in class net.sf.basedb.util.overview.loader.AutoChildNodeLoader

Call the same method on the 'parent' node loader.

createRootNode(DbControl, OverviewContext, I) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader

createRootNode(DbControl, OverviewContext, I) - Method in class net.sf.basedb.util.overview.loader.ExtensionChildNodeLoader

Call the same method on the 'parent' node loader.

createRootNode(DbControl, OverviewContext, I) - Method in interface net.sf.basedb.util.overview.loader.NodeLoader

Create a root node for the given item.

createRootNode(DbControl, OverviewContext, I) - Method in class net.sf.basedb.util.overview.loader.NullNodeLoader

createRootNode(DbControl, OverviewContext, DerivedBioAssay) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader

createRootNode(DbControl, OverviewContext, RawBioAssay) - Method in class net.sf.basedb.util.overview.loader.RawBioAssayLoader

createSchemaVersion(int) - Static method in class net.sf.basedb.core.Install

Create the schema version.

createSessionFactoryConfiguration(String, String, int, ClassLoader) - Method in class net.sf.basedb.core.ServiceSessionControl

Create an object that can be used for collecting configuration options and other settings that are needed to create session factories for services.

createSimpleEmail() - Static method in class net.sf.basedb.util.EmailUtil

Create a simple text email.

createSingleParentReverseNode(Extract, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader

Create a reverse-loading extract node from an extract.

createSingleParentReverseNode(MeasuredBioMaterial, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.SampleLoader

Create a reverse-loading sample node from an extract or sample.

createSlotManager() - Method in class net.sf.basedb.clients.jobagent.Agent

Create a slot manager and initialize it.

createSnapshot(DbControl, int) - Static method in class net.sf.basedb.core.AnnotationSet

Create a new annotation snapshot for the given annotation set.

createSoftware(String, String, String, ItemSubtypeData, UserData, ItemKeyData) - Static method in class net.sf.basedb.core.Install

Create a Software.

createSqlQuery(String) - Method in class net.sf.basedb.core.LogControl

Deprecated.

In 3.12. use LogControl.createSqlQuery(String, Class) instead

createSqlQuery(String, Class<R>) - Method in class net.sf.basedb.core.LogControl

Creates a Hibernate SQL query with a known return type.

createSqlQuery(Session, String) - Static method in class net.sf.basedb.core.HibernateUtil

Create a Hibernate SQL query.

createSqlQuery(Session, String, Class<R>) - Static method in class net.sf.basedb.core.HibernateUtil

Create a Hibernate SQL query with a known return type.

createSqlQuery(StatelessSession, String) - Static method in class net.sf.basedb.core.HibernateUtil

Create a Hibernate SQL query using a stateless session.

createSqlQuery(StatelessSession, String, Class<R>) - Static method in class net.sf.basedb.core.HibernateUtil

Create a Hibernate SQL query with a known return type using a stateless session.

createSQLQuery(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

If the same query has been executed before, return the cached instance, otherwise create a new query from the parent session and cache it.

createSQLQuery(String) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

If the same query has been executed before, return the cached instance, otherwise create a new query from the parent session and cache it.

createStandardHeaders(List<String>, ArrayDesign, List<ArrayDesignBlock>) - Method in class net.sf.basedb.plugins.GalExporter

Create the standard headers that are required by the GAL format or that are useful to have in the GAL file.

createStaticTables(SchemaGenerator.Mode, ProgressReporter) - Static method in class net.sf.basedb.core.HibernateUtil

Create the all tables in the database.

createStoredProcedureCall(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

createStoredProcedureCall(String) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

createStoredProcedureCall(String, Class...) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

createStoredProcedureCall(String, Class...) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

createStoredProcedureCall(String, String...) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

createStoredProcedureCall(String, String...) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

createStoredProcedureQuery(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

createStoredProcedureQuery(String, Class...) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

createStoredProcedureQuery(String, String...) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

createStyle() - Method in class net.sf.basedb.util.excel.CellStyleCreator

Create a new cell style.

createTables(SchemaGenerator.Mode, ProgressReporter, String, String) - Static method in class net.sf.basedb.core.Install

createTables(VirtualTable...) - Method in class net.sf.basedb.core.VirtualDb

Create the real database tables for this virtual database.

createTag(String, String, ItemSubtypeData, UserData, ItemKeyData) - Static method in class net.sf.basedb.core.Install

Create a Tag.

createTargetTypeQuery(DbControl) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

createTargetTypeRestriction(DbControl) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

createTempCollection(CollectionTransformer<?, ?>) - Method in class net.sf.basedb.util.collections.MultiStepCollectionTransformer

Create a temporary collection that is suitable for holding an intermediary result.

createTempDirectory(String, String, File) - Static method in class net.sf.basedb.util.FileUtil

Creates a temporary directory.

createTempIdTable(Set<Integer>) - Method in class net.sf.basedb.core.DbControl

Create a temporary table for holding given list of ID values.

createTemporaryWorkingDirectory() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

Create a temporary working directory in the local file system.

createTrustManagers(KeyStore, String, String) - Static method in class net.sf.basedb.util.ssl.SSLUtil2

createUnit(QuantityData, String, String, double, double, String, String...) - Static method in class net.sf.basedb.core.Install

Create a Unit.

createUpdateBatcher(Connection, String, int...) - Method in class net.sf.basedb.core.AnnotationBatcher

createUpdateBatcher(Connection, String, int...) - Method in class net.sf.basedb.core.MigrateRbaToDba

createUser(String, String, String, String, String, RoleData, QuotaData, boolean, boolean) - Static method in class net.sf.basedb.core.Install

Create a User.

createVirtualTable(VirtualDb, VirtualTable) - Static method in class net.sf.basedb.core.HibernateUtil

Create a table in the dynamic database.

CREATION - Enum constant in enum class net.sf.basedb.core.BioMaterialEvent.Type

An event of this type created a biomaterial.

creationEvent - Variable in class net.sf.basedb.core.data.MeasuredBioMaterialData

creationEvent - Variable in class net.sf.basedb.core.data.PhysicalBioAssayData

creationEvent - Variable in class net.sf.basedb.core.MeasuredBioMaterial

creationEvent - Variable in class net.sf.basedb.core.PhysicalBioAssay

creationTime - Variable in class net.sf.basedb.core.DiskUsageStatistics.Summary

CropStringMapper - Class in net.sf.basedb.util.parser

A mapper that crops a string if it is longer than a specified length.

CropStringMapper(Mapper, int) - Constructor for class net.sf.basedb.util.parser.CropStringMapper

Create a new CropStringMapper.

cropStrings - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

cropStrings - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

cropTooManyValues - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

crypt_raw(byte[], byte[], int, int[]) - Method in class net.sf.basedb.util.bcrypt.BCrypt

Perform the central password hashing step in the bcrypt scheme

cryptedPassword - Variable in class net.sf.basedb.core.data.PasswordData

cspHeader - Variable in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter

csvBytes - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo

cube - Variable in class net.sf.basedb.core.DynamicQuery

CUBE - Static variable in class net.sf.basedb.core.VirtualColumn

This column stores the data cube number.

cubeNo - Variable in class net.sf.basedb.core.data.DataCubeData

cubes - Variable in class net.sf.basedb.core.data.VirtualDbData

current - Variable in class net.sf.basedb.clients.web.taglib.Select

The currently selected item.

current - Variable in class net.sf.basedb.clients.web.taglib.SubtypeSelector

current - Variable in class net.sf.basedb.clients.web.taglib.table.ExtensionCells

current - Variable in class net.sf.basedb.util.NestedIterator

The current iterator.

current - Variable in class net.sf.basedb.util.query.MultiQueryIterator

CURRENT - Static variable in class net.sf.basedb.core.Quantity

The id for the Quantity object representing electric current.

currentAction - Variable in class net.sf.basedb.util.extensions.ActionIterator

CurrentAnnotationInfo(AnnotationType, Item) - Constructor for class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo

currentAnnotationSetId - Variable in class net.sf.basedb.core.AnnotationBatcher

currentClient - Variable in class net.sf.basedb.core.SessionControl

Information about the current ClientData that checked out this SessionControl.

currentContext - Variable in class net.sf.basedb.util.extensions.ActionIterator

currentContexts - Variable in class net.sf.basedb.core.SessionControl

Map for storing current contexts.

currentFile - Variable in class net.sf.basedb.plugins.AbstractFlatFileImporter

currentFilename - Variable in class net.sf.basedb.clients.web.fileupload.FileUploadProgress

currentImageRemapper - Static variable in class net.sf.basedb.clients.web.extensions.skin.ImageRemapperUtil

currentIndex - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter.FileIterator

currentInfo - Variable in class net.sf.basedb.core.AnnotationBatcher

currentItem - Variable in class net.sf.basedb.core.AnnotationBatcher

currentPage - Variable in class net.sf.basedb.clients.web.taglib.table.Navigator

The current page.

currentParticipant - Variable in class net.sf.basedb.util.overview.node.BioPlateNameGenerator

currentPosition - Variable in class net.sf.basedb.core.FeatureBatcher

Keeps track of the position number.

currentPosition - Variable in class net.sf.basedb.core.RawDataBatcher

Keeps track of the position number unless the raw bioassay is connected to an array design with features.

currentPosition - Variable in class net.sf.basedb.util.importer.spotdata.PositionEventHandler

currentRow - Variable in class net.sf.basedb.clients.web.plugins.XlsxTemplate

currentRow - Variable in class net.sf.basedb.util.excel.XlsxTableWriter

currentSection - Variable in class net.sf.basedb.util.basefile.BaseFileWriter

currentSection - Variable in class net.sf.basedb.util.bfs.MetadataModel

currentSection - Variable in class net.sf.basedb.util.bfs.MetadataWriter

currentSheet - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil.WorkbookStream

currentStream - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil.WorkbookStream

currentSubCategory - Variable in class net.sf.basedb.clients.web.taglib.SubtypeSelector

currentSubcontexts - Variable in class net.sf.basedb.core.SessionControl

Current active subcontext names.

currentWell - Variable in class net.sf.basedb.util.overview.node.BioPlateNameGenerator

currentWell - Variable in class net.sf.basedb.util.overview.node.BioWellNameGenerator

currentXt - Variable in class net.sf.basedb.util.extensions.ClientContext

currentXtPoint - Variable in class net.sf.basedb.util.extensions.ClientContext

CurvedScaleFactor(long) - Constructor for class net.sf.basedb.util.InputStreamTracker.CurvedScaleFactor

CustomRequestHandler - Interface in net.sf.basedb.clients.jobagent.handlers

An extension to the regular request-handler interface that allows life-cycle control by the job agent.

customRequestHandlerClasses - Variable in class net.sf.basedb.clients.jobagent.Agent

D

data - Variable in class net.sf.basedb.clients.web.taglib.table.Row

The parent <tbl:data> tag.

data - Variable in class net.sf.basedb.core.BasicItem

The data class from the net.sf.basedb.core.data layer that holds the data for this item.

data - Variable in class net.sf.basedb.core.BioMaterialEventSource

data - Variable in class net.sf.basedb.core.ChangeHistory.TransactionInfo

data - Variable in class net.sf.basedb.core.Coloring

data - Variable in class net.sf.basedb.core.DataResultIterator

The internal iterator of BasicData objects.

data - Variable in class net.sf.basedb.core.ItemResultIterator

The internal iterator of BasicData objects.

data - Variable in class net.sf.basedb.core.ItemResultList

The internal list of BasicData objects.

data - Variable in class net.sf.basedb.core.ReporterScore

data - Variable in class net.sf.basedb.core.ReporterScoreResultIterator

The internal iterator of data layer objects.

data - Variable in class net.sf.basedb.util.bfs.AnnotationModel

data - Variable in class net.sf.basedb.util.bfs.MatrixModel

data - Variable in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser.SynchronizedData

data - Variable in class net.sf.basedb.util.parser.ColFunction

data - Variable in class net.sf.basedb.util.parser.DataNoFunction

data - Variable in class net.sf.basedb.util.parser.LineNoFunction

data() - Method in class net.sf.basedb.util.parser.FlatFileParser.Data

The data line as an array of strings.

Data - Class in net.sf.basedb.clients.web.taglib.table

This tag begins the data section of the table.

Data() - Constructor for class net.sf.basedb.clients.web.taglib.table.Data

Data(int, int, String, String[], boolean, boolean, boolean) - Constructor for class net.sf.basedb.util.parser.FlatFileParser.Data

Create a new data object.

DATA - Enum constant in enum class net.sf.basedb.util.parser.FlatFileParser.LineType

The parsed line is a data line, which could be split into the specified number of columns by FlatFileParser.setDataSplitterRegexp(Pattern).

DATA_EVENT - Static variable in class net.sf.basedb.util.bfs.AnnotationParser

Event thep that is issued for each data line.

DATA_EVENT - Static variable in class net.sf.basedb.util.bfs.DataParser

Event type that is issued for each data line.

DATA_EVENT - Static variable in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser

Event type that is issued for each data line.

DATA_FILE - Enum constant in enum class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext.Type

The context is a list with data-files that are attached to a parent item.

DATA_FILES - Variable in class net.sf.basedb.core.PropertyFilter

DATA_FOOTER - Enum constant in enum class net.sf.basedb.util.parser.FlatFileParser.LineType

The parsed line is the data footer line, matching the regular expression specified by FlatFileParser.setDataFooterRegexp(Pattern).

DATA_HEADER - Enum constant in enum class net.sf.basedb.util.parser.FlatFileParser.LineType

The parsed line is the data header line, matching the regular expression specified by FlatFileParser.setDataHeaderRegexp(Pattern).

DatabaseException - Exception in net.sf.basedb.core

Exceptions of this type are thrown when there is an error from the database.

DatabaseException() - Constructor for exception net.sf.basedb.core.DatabaseException

Create a new DatabaseException object.

DatabaseException(String) - Constructor for exception net.sf.basedb.core.DatabaseException

Create a new DatabaseException object with the specified message.

DatabaseException(String, Throwable) - Constructor for exception net.sf.basedb.core.DatabaseException

Create a new DatabaseException object with the specified message

DatabaseException(Throwable) - Constructor for exception net.sf.basedb.core.DatabaseException

Create a new DatabaseException object acting as a wrapper for another exception that caused the error.

databaseVersionNumber - Static variable in class net.sf.basedb.core.Application

The name and version of the database server

dataClass - Variable in class net.sf.basedb.core.BasicBatcher

The class of data objects accepted by this batcher.

dataClass - Variable in class net.sf.basedb.core.DataQuery

The class of the data objects that are returned.

dataClass - Variable in class net.sf.basedb.core.DataResultIterator

The class of the data objects returned by the query (and this object).

dataClass - Variable in enum class net.sf.basedb.core.Item

dataClass - Variable in class net.sf.basedb.core.ItemQuery

The data layer class of the item objects that are returned.

dataClassMapping - Static variable in enum class net.sf.basedb.core.Item

dataCube - Variable in class net.sf.basedb.core.data.DataCubeColumnData

dataCube - Variable in class net.sf.basedb.core.data.DataCubeExtraValueData

dataCube - Variable in class net.sf.basedb.core.data.DataCubeFilterData

dataCube - Variable in class net.sf.basedb.core.data.DataCubeLayerData

dataCube - Variable in class net.sf.basedb.core.MappingBatcher

The datacube this batcher inserts data for.

dataCube - Variable in class net.sf.basedb.core.PositionBatcher

The datacube this batcher inserts data for.

DataCube - Class in net.sf.basedb.core

A data cube is the main unit for an experiment to store analysed data.

DataCube(DataCubeData) - Constructor for class net.sf.basedb.core.DataCube

Creates a new data cube item from the given data.

DATACUBE - Enum constant in enum class net.sf.basedb.core.Item

The item is a DataCube

DataCube.RawMappingQuery - Class in net.sf.basedb.core

Select data from Dynamic#RawParents table.

dataCubeColumn - Variable in class net.sf.basedb.core.data.BioAssayData

DataCubeColumn - Class in net.sf.basedb.core

Represents the column coordinate in a data cube.

DataCubeColumn(DataCubeColumnData) - Constructor for class net.sf.basedb.core.DataCubeColumn

Creates a new data cube item from the given data.

DATACUBECOLUMN - Enum constant in enum class net.sf.basedb.core.Item

The item is a DataCubeColumn

DataCubeColumnData - Class in net.sf.basedb.core.data

This class holds information about a single column in a data cube.

DataCubeColumnData() - Constructor for class net.sf.basedb.core.data.DataCubeColumnData

DataCubeData - Class in net.sf.basedb.core.data

This class holds information about a single data cube in a virtual database.

DataCubeData() - Constructor for class net.sf.basedb.core.data.DataCubeData

dataCubeExtraValue - Variable in class net.sf.basedb.core.data.ExtraValueData

DataCubeExtraValue - Class in net.sf.basedb.core

Represents a set of extra value in a data cube.

DataCubeExtraValue(DataCubeExtraValueData) - Constructor for class net.sf.basedb.core.DataCubeExtraValue

Creates a new data cube item from the given data.

DATACUBEEXTRAVALUE - Enum constant in enum class net.sf.basedb.core.Item

The item is a DataCubeExtraValue

DataCubeExtraValueData - Class in net.sf.basedb.core.data

This class holds information about an extra value in a data cube.

DataCubeExtraValueData() - Constructor for class net.sf.basedb.core.data.DataCubeExtraValueData

dataCubeFilter - Variable in class net.sf.basedb.core.data.BioAssaySetData

DataCubeFilter - Class in net.sf.basedb.core

This represents a filter in a datacube.

DataCubeFilter(DataCubeFilterData) - Constructor for class net.sf.basedb.core.DataCubeFilter

Creates a new data cube item from the given data.

DATACUBEFILTER - Enum constant in enum class net.sf.basedb.core.Item

The item is a DataCubeFilter

DataCubeFilterData - Class in net.sf.basedb.core.data

This class holds information about a single filter in a data cube.

DataCubeFilterData() - Constructor for class net.sf.basedb.core.data.DataCubeFilterData

dataCubeLayer - Variable in class net.sf.basedb.core.data.BioAssaySetData

DataCubeLayer - Class in net.sf.basedb.core

This represents the layer coordinate in a data cube.

DataCubeLayer(DataCubeLayerData) - Constructor for class net.sf.basedb.core.DataCubeLayer

Creates a new data cube item from the given data.

DATACUBELAYER - Enum constant in enum class net.sf.basedb.core.Item

The item is a DataCubeLayer

DataCubeLayerData - Class in net.sf.basedb.core.data

This class holds information about a single layer in a data cube.

DataCubeLayerData() - Constructor for class net.sf.basedb.core.data.DataCubeLayerData

dataCubes - Variable in class net.sf.basedb.core.data.VirtualDbData

dataDirectory - Variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter

dataDirectory - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

dataDirectory - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

dataFile(BasicItem) - Static method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext

Creates a data-file listing context where files belong to a parent item.

DATAFILE_INVALID - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if a data file is valid.

DATAFILE_INVALID_ITEM - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if a data file can be used on the current item type.

DATAFILE_NOTPLATFORM - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if a file is registered with a platform/item subtype or not.

DATAFILE_NOTVALIDATED - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if a data file has been validated or not.

DATAFILE_TOOMANYFILES - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if there are more than one file of a file type that doesn't allow multiple files.

DataFileFormatter - Class in net.sf.basedb.clients.web.formatter

Formatter implementation for file sets that lists all member files of a given file type

DataFileFormatter(DbControl, DataFileType, ModeInfo) - Constructor for class net.sf.basedb.clients.web.formatter.DataFileFormatter

Creates a new formatter instance for the given file type and list mode.

DataFileFormatter(DbControl, DataFileType, ModeInfo, FileViewerUtil) - Constructor for class net.sf.basedb.clients.web.formatter.DataFileFormatter

Creates a new formatter instance for the given file type and list mode.

DataFileLoader - Class in net.sf.basedb.util.overview.loader

Node loader implementation for data files.

DataFileLoader() - Constructor for class net.sf.basedb.util.overview.loader.DataFileLoader

DataFileType - Class in net.sf.basedb.core

This class is used to represent types of files that are used to hold data instead of importing the data into into the database.

DataFileType(DataFileTypeData) - Constructor for class net.sf.basedb.core.DataFileType

Creates a new filetype item from the given data.

DATAFILETYPE - Enum constant in enum class net.sf.basedb.core.Item

The item is a DataFileType

DataFileTypeData - Class in net.sf.basedb.core.data

This class hols information about individual files attached to items that store data in files instead of in the database.

DataFileTypeData() - Constructor for class net.sf.basedb.core.data.DataFileTypeData

DataFileValidator - Class in net.sf.basedb.util.overview.validator

Validator implementation for data files.

DataFileValidator() - Constructor for class net.sf.basedb.util.overview.validator.DataFileValidator

dataFooter - Variable in class net.sf.basedb.util.parser.FlatFileParser

The regular expression for matching the data footer line.

dataFooterRegexpParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter

Parameter definition that asks for the regular expression that matches the data footer.

dataFormat - Variable in class net.sf.basedb.util.excel.CellStyleCreator

dataFormat - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo

dataHeader - Variable in class net.sf.basedb.util.parser.FlatFileParser

The regular expression for matching the data header line.

dataHeaderRegexpParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter

Parameter definition that asks for the regular expression that matches the data header.

dataLineNo - Variable in class net.sf.basedb.util.parser.FlatFileParser.Data

dataLineNo() - Method in class net.sf.basedb.util.parser.FlatFileParser.Data

The line number of the data in the current section.

dataloader - Variable in class net.sf.basedb.clients.web.plugins.ExportedProperty

DataLoader<T> - Interface in net.sf.basedb.clients.web.plugins

A helper interface for the SimpleExport to get data that in some way are associated with an item.

dataNoFunction - Variable in class net.sf.basedb.util.parser.JepMapper

DataNoFunction - Class in net.sf.basedb.util.parser

Adds a dataNo() function to Jep.

DataNoFunction() - Constructor for class net.sf.basedb.util.parser.DataNoFunction

DataParser - Class in net.sf.basedb.util.bfs

Parser implementation that parses BFS data files.

DataParser() - Constructor for class net.sf.basedb.util.bfs.DataParser

Create a new data parser.

dataParsers - Variable in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser

dataPart - Variable in class net.sf.basedb.util.basefile.BaseFileWriter

DataQuery<I extends BasicData> - Class in net.sf.basedb.core

An implementation of the Query interface that returns data objects.

DataQuery(Class<I>, String) - Constructor for class net.sf.basedb.core.DataQuery

Create a new query for the specified item, using the default optional runtime filter.

DataQuery(Class<I>, Item, String, String) - Constructor for class net.sf.basedb.core.DataQuery

Create a query that may have different return type and root entity.

DataQueryWrapper - Class in net.sf.basedb.clients.web.plugins

A query wrapper for DataQuery:s.

DataQueryWrapper(DataQuery<BasicData>) - Constructor for class net.sf.basedb.clients.web.plugins.DataQueryWrapper

Create a new query wrapper.

DataResultIterator<I extends BasicData> - Class in net.sf.basedb.core

Return the results of a DataQuery as an iterator.

DataResultIterator(ScrollIterator<I>, SessionControl, Session, Class<I>, long) - Constructor for class net.sf.basedb.core.DataResultIterator

dataSeparator - Variable in class net.sf.basedb.util.export.TableWriter

dataSplitter - Variable in class net.sf.basedb.util.parser.FlatFileParser

The regular expression for splitting a data line.

dataSplitterRegexpParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter

Parameter definition that asks for the regular expression that splits a data line into individual columns.

datatype - Variable in class net.sf.basedb.clients.web.taglib.table.TableColumn

DataWriter - Class in net.sf.basedb.util.bfs

Writer implementation for writing BFS data files.

DataWriter(Writer) - Constructor for class net.sf.basedb.util.bfs.DataWriter

Create a new BFS data writer.

dataWriterFactory - Variable in class net.sf.basedb.util.export.spotdata.BfsExporter

DataWriterFactory<T> - Interface in net.sf.basedb.util.bfs

Factory implementations are responsible for creating BFS data writers that accepts data for a given owner object.

dataWriters - Variable in class net.sf.basedb.util.export.spotdata.BfsExporter

DATE - Enum constant in enum class net.sf.basedb.core.Type

The parameter is a date value.

DATE - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper

DATE_FORMAT - Static variable in class net.sf.basedb.core.DateUtil

DATE_FORMAT - Static variable in class net.sf.basedb.core.log.EntityDetails

DATE_FORMAT_ERROR - Static variable in class net.sf.basedb.plugins.util.Parameters

The name of the parameter created by Parameters.dateFormatError(String, String, String, String...).

DATE_FORMAT_PARAMETER - Static variable in class net.sf.basedb.plugins.util.Parameters

The name of the parameter that is created by Parameters.dateFormatParameter(String, String, String)

DateCopyPropertyPath(Type) - Constructor for class net.sf.basedb.core.Metadata.DateCopyPropertyPath

dateFormat - Variable in class net.sf.basedb.core.migrate.DateWriter

dateFormat - Variable in class net.sf.basedb.core.migrate.postgres.PostgresResultWriterFactory

PostgreSQL uses 'yyyy-MM-dd' for dates.

dateFormat - Variable in class net.sf.basedb.core.migrate.TimestampWriter

dateFormat - Variable in class net.sf.basedb.util.excel.AutoFormatter

dateFormat - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil

dateFormat - Variable in class net.sf.basedb.util.formatter.DateFormatter

dateFormat - Variable in class net.sf.basedb.util.parser.ColFunction

dateFormat - Variable in class net.sf.basedb.util.parser.FlatFileParser

The default date formatter to use when creating mappers.

dateFormat - Variable in class net.sf.basedb.util.parser.JepMapper

dateFormatError(String, String, String, String...) - Static method in class net.sf.basedb.plugins.util.Parameters

Create the parameter for handling invalid dates/timestamps.

dateFormatErrorParameter - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

DateFormatException - Exception in net.sf.basedb.core

This exception is thrown when parsing a string into a date failed.

DateFormatException(String) - Constructor for exception net.sf.basedb.core.DateFormatException

Creates a new DateFormatException.

DateFormatException(String, Throwable) - Constructor for exception net.sf.basedb.core.DateFormatException

Creates a new DateFormatException.

dateFormatParameter(String, String, String) - Static method in class net.sf.basedb.plugins.util.Parameters

Parameter definition that asks for the format used by date values when parsed from strings.

dateFormatter - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

dateFormatter - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

dateFormatter - Variable in class net.sf.basedb.util.formatter.PropertyFilterFormatter

DateFormatter - Class in net.sf.basedb.util.formatter

Format a date for output in a client application.

DateFormatter(String) - Constructor for class net.sf.basedb.util.formatter.DateFormatter

Create a new date formatter.

DateFormatter(DateFormat) - Constructor for class net.sf.basedb.util.formatter.DateFormatter

Create a new date formatter.

DateParameterType - Class in net.sf.basedb.core

This class represent a parameter type that is a date.

DateParameterType() - Constructor for class net.sf.basedb.core.DateParameterType

Create a new date parameter type, allowing null values.

DateParameterType(Date, boolean) - Constructor for class net.sf.basedb.core.DateParameterType

Create a new date parameter type.

DateParameterType(Date, boolean, int, int, int, List<Date>) - Constructor for class net.sf.basedb.core.DateParameterType

Creates a new DateParameterType

DateParameterValueData - Class in net.sf.basedb.core.data

Date parameter value.

DateParameterValueData() - Constructor for class net.sf.basedb.core.data.DateParameterValueData

DateParameterValueData(Date...) - Constructor for class net.sf.basedb.core.data.DateParameterValueData

dateParser - Variable in class net.sf.basedb.util.parser.ColumnMapper

dateParser - Variable in class net.sf.basedb.util.parser.CompoundMapper

dateParser - Variable in class net.sf.basedb.util.parser.ConstantMapper

DATETIME_FORMAT - Static variable in class net.sf.basedb.core.log.EntityDetails

DateUtil - Class in net.sf.basedb.core

Utility methods that will make it easier to handle date values.

DateUtil() - Constructor for class net.sf.basedb.core.DateUtil

DateValue(Date, String) - Constructor for class net.sf.basedb.util.excel.ExcelValue.DateValue

DateWriter - Class in net.sf.basedb.core.migrate

Generic writer implementation that writes date values from a result set.

DateWriter(ResultSet, int, Writer, char[], FastDateFormat) - Constructor for class net.sf.basedb.core.migrate.DateWriter

dbaId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba

DbCleaner() - Constructor for class net.sf.basedb.core.Application.DbCleaner

DbControl - Class in net.sf.basedb.core

A DbControl object is the main object used for communicating with the database.

DbControl(SessionControl, String) - Constructor for class net.sf.basedb.core.DbControl

Create a new object.

DbControl.SaveIf - Class in net.sf.basedb.core

DbControl.State - Class in net.sf.basedb.core

Main purpose is to write a warning to the log file in case some user code that created a DbControl instance never called the close() method before the DbControl became uncreachable.

dbControlCache - Variable in class net.sf.basedb.core.SessionControl

Holds all created DbControl object, so we can close them if the user logs out.

dbEngine - Variable in class net.sf.basedb.core.hibernate.DbIndexWork

dbEngine - Variable in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget

dbEngine - Variable in class net.sf.basedb.core.hibernate.SchemaGenerator

dbEngine - Static variable in class net.sf.basedb.core.HibernateUtil

Our extra database specific sql generation that is not possible by the Hibernate dialect.

DbEngine - Interface in net.sf.basedb.core.dbengine

Information about database-specific options that are not covered by the Hibernate Dialect objects.

dbFeatures - Variable in class net.sf.basedb.core.data.ArrayDesignData

dbIndexes(boolean, boolean, boolean, boolean) - Static method in class net.sf.basedb.core.HibernateUtil

Prints a lot of useful stuff about the database to standard output.

DbIndexWork - Class in net.sf.basedb.core.hibernate

A work implementation that can create, update and drop indexes on tables.

DbIndexWork(Metadata, Dialect, DbEngine, boolean, boolean, boolean, boolean) - Constructor for class net.sf.basedb.core.hibernate.DbIndexWork

DbLogManager - Class in net.sf.basedb.core.log.db

Log manager implementation that logs changes to the database.

DbLogManager(LogControl) - Constructor for class net.sf.basedb.core.log.db.DbLogManager

DbLogManagerFactory - Class in net.sf.basedb.core.log.db

Log manager factory implementationt that logs changes to the database.

DbLogManagerFactory() - Constructor for class net.sf.basedb.core.log.db.DbLogManagerFactory

DbLogManagerFactory(boolean, boolean) - Constructor for class net.sf.basedb.core.log.db.DbLogManagerFactory

dc - Variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl

dc - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper

dc - Variable in class net.sf.basedb.clients.web.formatter.DataFileFormatter

dc - Variable in class net.sf.basedb.clients.web.plugins.SimpleExport

dc - Variable in class net.sf.basedb.clients.web.taglib.PropertyValue

A DbControl object.

dc - Variable in class net.sf.basedb.clients.web.taglib.SubtypeSelector

dc - Variable in class net.sf.basedb.clients.web.taglib.table.ExtensionCells

dc - Variable in class net.sf.basedb.core.AbstractBatcher

A reference to the current DbControl object.

dc - Variable in class net.sf.basedb.core.AnyToAny.FastLinkLoader

dc - Variable in class net.sf.basedb.core.BasicItem

A reference to the current DbControl object.

dc - Variable in class net.sf.basedb.core.BioMaterialEventSource

dc - Variable in class net.sf.basedb.core.DerivedBioAssay.FixDerivedBioAssayParentsRecursivelyAction

dc - Variable in class net.sf.basedb.core.DiskUsageStatistics

dc - Variable in class net.sf.basedb.core.FastAnnotationLoader

dc - Variable in class net.sf.basedb.core.FastAnnotationLoader.FastIterator

dc - Variable in class net.sf.basedb.core.ItemResultIterator

The DbControl tthat was used in the query.

dc - Variable in class net.sf.basedb.core.ItemResultList

The DbControl that was used in the query.

dc - Variable in class net.sf.basedb.core.LogControl

dc - Variable in class net.sf.basedb.core.MeasuredBioMaterial.RemainingQuantityAction

dc - Variable in class net.sf.basedb.core.MigrateRbaToDba

dc - Variable in class net.sf.basedb.core.ReporterScoreResultIterator

The DbControl that was used in the query.

dc - Variable in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil

dc - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot.AnnotationTypeComparator

dc - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot.ProjectComparator

dc - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

dc - Variable in class net.sf.basedb.plugins.BaseFileExporterPlugin

dc - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

dc - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

dc - Variable in class net.sf.basedb.plugins.BfsExporterPlugin

dc - Variable in class net.sf.basedb.plugins.GalExporter

dc - Variable in class net.sf.basedb.plugins.HelpExporter

dc - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter

dc - Variable in class net.sf.basedb.plugins.PackedFileExporter

dc - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter

dc - Variable in class net.sf.basedb.plugins.PlateMappingExporter

dc - Variable in class net.sf.basedb.plugins.PlateMappingImporter

dc - Variable in class net.sf.basedb.plugins.PluginConfigurationExporter

dc - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter

dc - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

dc - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

dc - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

dc - Variable in class net.sf.basedb.util.affymetrix.CdfValidationAction

dc - Variable in class net.sf.basedb.util.affymetrix.CelValidationAction

dc - Variable in class net.sf.basedb.util.annotations.InheritAnnotationsManager

dc - Variable in class net.sf.basedb.util.bfs.BaseInputStreamLocator

dc - Variable in class net.sf.basedb.util.bfs.GenericBaseDataWriterFactory

dc - Variable in class net.sf.basedb.util.bfs.GenericExtraFileImporter

dc - Variable in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

dc - Variable in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter

dc - Variable in class net.sf.basedb.util.extensions.ClientContext

dc - Variable in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor

dc - Variable in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor

dc - Variable in class net.sf.basedb.util.formatter.PropertyFilterFormatter

dc - Variable in class net.sf.basedb.util.gtf.GtfValidationAction

dc - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileImporter

dc - Variable in class net.sf.basedb.util.importer.spotdata.BfsImporter

dc - Variable in class net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser

dc - Variable in class net.sf.basedb.util.importer.spotdata.SecondPassSectionSpotsParser

dc - Variable in class net.sf.basedb.util.importer.spotdata.SectionAssaysParser

dc - Variable in class net.sf.basedb.util.importer.spotdata.SectionReporterListParser

dc - Variable in class net.sf.basedb.util.jep.ExtraValueFunction

dc - Variable in class net.sf.basedb.util.jep.InReporterListFunction

dc - Variable in class net.sf.basedb.util.jep.MeanFunction

dc - Variable in class net.sf.basedb.util.jep.NotInReporterListFunction

dc - Variable in class net.sf.basedb.util.jep.RawFunction

dc - Variable in class net.sf.basedb.util.jep.ReporterFunction

dc - Variable in class net.sf.basedb.util.jep.ScoreFunction

dc - Variable in class net.sf.basedb.util.listable.TransformContext

dc - Variable in class net.sf.basedb.util.overview.node.NodeFactory

dc - Variable in class net.sf.basedb.util.parser.DefaultItemFunction

dc - Variable in class net.sf.basedb.util.query.MultiQueryIterator

dc - Variable in class net.sf.basedb.util.units.UnitCache

dc - Variable in class net.sf.basedb.util.zip.ZipUnpacker

debug - Static variable in class net.sf.basedb.util.overview.GenericOverview

debug - Static variable in class net.sf.basedb.util.overview.loader.AbstractNodeLoader

debug - Static variable in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader

debug - Static variable in class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory

debug - Static variable in class net.sf.basedb.util.overview.node.NodeFactory

debug(String) - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLogger

Log a DEBUG message.

debug(String, Throwable) - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLogger

Log a DEBUG message with an optional stacktrace.

DEBUG - Enum constant in enum class net.sf.basedb.util.extensions.logging.LogLevel

DEBUG - Enum constant in enum class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory.Level

debugEnabled - Static variable in class net.sf.basedb.core.AbstractEntityQuery

So we don't always have to call logParam.debug()

debugEnabled - Static variable in class net.sf.basedb.core.AbstractHqlQuery

So we don't always have to call logParam.debug()

debugEnabled - Static variable in class net.sf.basedb.core.AbstractQuery

So we don't always have to call logSql.debug()

debugEnabled - Static variable in class net.sf.basedb.core.BasicBatcher

So we don't always have to call logParam.debug()

debugEnabled - Static variable in class net.sf.basedb.core.BatchUtil

So we don't always have to call logSql.debug()

DebugOnSaveAction(JspContext) - Constructor for class net.sf.basedb.clients.web.extensions.edit.DebugOnSaveActionFactory.DebugOnSaveAction

DebugOnSaveActionFactory - Class in net.sf.basedb.clients.web.extensions.edit

On-save action factory that create actions that print a log message to System.out for all events.

DebugOnSaveActionFactory() - Constructor for class net.sf.basedb.clients.web.extensions.edit.DebugOnSaveActionFactory

DebugOnSaveActionFactory.DebugOnSaveAction - Class in net.sf.basedb.clients.web.extensions.edit

debugParamEnabled - Static variable in class net.sf.basedb.core.AbstractSqlQuery

So we don't always have to call logParam.debug()

debugSqlEnabled - Static variable in class net.sf.basedb.core.AbstractBatcher

So we don't always have to call logSql.debug()

debugSqlEnabled - Static variable in class net.sf.basedb.core.AbstractSqlQuery

So we don't always have to call logSql.debug()

debugSqlEnabled - Static variable in class net.sf.basedb.core.AnnotationRestriction

So we don't always have to call logSql.debug()

debugSqlEnabled - Static variable in class net.sf.basedb.core.RawDataBatcher

So we don't always have to call logSql.debug()

debugSqlEnabled - Static variable in class net.sf.basedb.core.VirtualDb

So we don't always have to call logSql.debug()

decapitalize(String) - Static method in class net.sf.basedb.core.StringUtil

Decapitalize the string by making sure the first character is lower-case.

decideOnFirst - Variable in class net.sf.basedb.util.formatter.MultiFormatter

DECIMAL_SEPARATOR_PARAMETER - Static variable in class net.sf.basedb.plugins.util.Parameters

The name of the parameter that is created by Parameters.decimalSeparatorParameter(String, String, String)

decimalSeparatorParameter(String, String, String) - Static method in class net.sf.basedb.plugins.util.Parameters

Parameter definition that asks for the decimal separator used by numeric values when parsed from strings.

decode(String) - Method in interface net.sf.basedb.util.encode.EncoderDecoder

decode(String) - Method in class net.sf.basedb.util.encode.IdentityEncoderDecoder

decode(String) - Method in class net.sf.basedb.util.encode.TabCrLfEncoderDecoder

decode(String) - Method in class net.sf.basedb.util.encode.ToSpaceEncoderDecoder

decode_base64(String, int) - Static method in class net.sf.basedb.util.bcrypt.BCrypt

Decode a string encoded using bcrypt's base64 scheme to a byte array.

decodeAll(Collection<String>, EncoderDecoder) - Static method in class net.sf.basedb.util.encode.EncodeUtil

Decode all strings in a collection.

decoder - Variable in class net.sf.basedb.util.bfs.AnnotationParser

decoder - Variable in class net.sf.basedb.util.bfs.DataParser

decoder - Variable in class net.sf.basedb.util.bfs.MetadataParser

decodeValue(String) - Method in class net.sf.basedb.util.bfs.AnnotationParser

Decode an encoded value.

decodeValue(String) - Method in class net.sf.basedb.util.bfs.DataParser

Decode an encoded value.

decodeValue(String) - Method in class net.sf.basedb.util.bfs.MetadataParser

Decode an encoded value.

decompress(ProgressReporter) - Method in class net.sf.basedb.core.File

Decompress the file stored on the disk.

deepCopy(Node) - Method in class net.sf.basedb.util.overview.Node

Create a deep copy of this node and all it's children.

deepCopyInternal(Node) - Method in class net.sf.basedb.util.overview.Node

DEFAULT - Static variable in class net.sf.basedb.clients.web.ModeInfo

DEFAULT - Static variable in class net.sf.basedb.core.Application.StartupOptions

Default startup options that will start BASE for normal operations using the options specified in "base.config".

DEFAULT - Static variable in class net.sf.basedb.core.Quota

The ID for the system default quota, which is assigned to new users unless another quota is specified.

DEFAULT_CHECK_INTERVAL - Static variable in class net.sf.basedb.clients.jobagent.Agent

The default check interval in seconds.

DEFAULT_DATE_FORMAT - Static variable in class net.sf.basedb.clients.web.formatter.FormatterSettings

The default date format for a date formatter = @value

DEFAULT_DATETIME_FORMAT - Static variable in class net.sf.basedb.clients.web.formatter.FormatterSettings

The default datetime format for a datetime formatter = @value

DEFAULT_ERROR - Static variable in class net.sf.basedb.plugins.util.Parameters

The name of the parameter created by Parameters.defaultError(String, String, String, String...).

DEFAULT_FILTER - Static variable in class net.sf.basedb.util.extensions.Registry

Default filter implementation for Registry.useExtensions(ClientContext, ExtensionsFilter, String...)

DEFAULT_JOB_EXECUTOR - Static variable in class net.sf.basedb.clients.jobagent.Agent

The default job executor to use if none has been specified in the configuration file.

DEFAULT_LOGIN - Static variable in class net.sf.basedb.clients.web.extensions.login.FieldInfo

This is the default login field.

DEFAULT_MAX_UNKNOWN_LINES - Static variable in class net.sf.basedb.util.parser.FlatFileParser

The default value for the number of unknown lines in a row that may be encountered by the parseHeaders method before it gives up.

DEFAULT_NAME - Static variable in class net.sf.basedb.core.ItemContext

This is the name of the default context which is automatically saved when a user is logging out.

DEFAULT_NUM_DECIMALS - Static variable in class net.sf.basedb.clients.web.formatter.FormatterSettings

The default number of decimals to display by a number formatter = @value

DEFAULT_PAGE_TITLE - Static variable in class net.sf.basedb.clients.web.taglib.Page

The default page title.

DEFAULT_PASSWORD - Static variable in class net.sf.basedb.clients.web.extensions.login.FieldInfo

This is the default password field.

DEFAULT_PORT - Static variable in class net.sf.basedb.core.JobAgent

The default port (47822) where job agents are listening for connections.

DEFAULT_SLOT_MANAGER - Static variable in class net.sf.basedb.clients.jobagent.Agent

The default slot manager to use if none has been specified in the configuration file.

DEFAULT_TIMEOUT - Static variable in class net.sf.basedb.clients.web.fileupload.FileUpload

The default timeout to use when waiting for the next data packet to arrive.

defaultArrayDesignFunction - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

DefaultConfigurationValues - Class in net.sf.basedb.plugins.gtf

Provides a default configuration values for GTF file parsing when none has been provided by the user.

DefaultConfigurationValues(ParameterValues) - Constructor for class net.sf.basedb.plugins.gtf.DefaultConfigurationValues

DefaultDbEngine - Class in net.sf.basedb.core.dbengine

A default DbEngine that is selected if no other can be found.

DefaultDbEngine() - Constructor for class net.sf.basedb.core.dbengine.DefaultDbEngine

Create DefaultDbEngine.

defaultDeleted(int, boolean) - Method in class net.sf.basedb.core.ProjectSpecificAnnotationsManager

A default annotation is being deleted in this transaction.

DefaultEntityLogger - Class in net.sf.basedb.core.log.db

Default logger for all entities that has been tagged with the LoggableData interface.

DefaultEntityLogger(DbLogManagerFactory) - Constructor for class net.sf.basedb.core.log.db.DefaultEntityLogger

Creates a new entity logger.

defaultError(String, String, String, String...) - Static method in class net.sf.basedb.plugins.util.Parameters

Create the default error handling parameter.

defaultErrorHandler - Variable in class net.sf.basedb.util.error.ClassMapErrorHandler

defaultErrorHandlerFactory - Variable in class net.sf.basedb.util.extensions.Registry

defaultErrorParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter

defaultErrorParameter - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

DefaultFilter - Class in net.sf.basedb.util.extensions

A default filter implementation that enables all extensions and extension points and sorts the extensions based on the Extension.getIndex() values.

DefaultFilter() - Constructor for class net.sf.basedb.util.extensions.DefaultFilter

Create a new default filter.

defaultFirst - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot.ProjectComparator

defaultFormat - Variable in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet

defaultFormat - Variable in class net.sf.basedb.clients.web.servlet.PlotServlet

defaultFormatter - Variable in class net.sf.basedb.util.formatter.MultiFormatter

defaultGuiContexts - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

The default gui contexts where it makes sense to use an analysis plugin.

defaultHandler - Variable in class net.sf.basedb.clients.jobagent.handlers.MultiProtocolRequestHandler

defaultHardwareFunction - Variable in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter

defaultHardwareFunction - Variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter

defaultHardwareFunction - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

defaultHardwareFunction - Variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter

defaultHeight - Variable in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet

defaultHeight - Variable in class net.sf.basedb.clients.web.servlet.PlotServlet

defaultIds - Static variable in class net.sf.basedb.clients.web.taglib.Button

defaultImages - Static variable in class net.sf.basedb.clients.web.taglib.Button

DefaultItemFunction<T extends Nameable> - Class in net.sf.basedb.util.parser

JEP function that can be used to return the name of a default item in a project.

DefaultItemFunction(DbControl, Project, Item) - Constructor for class net.sf.basedb.util.parser.DefaultItemFunction

Create a new function instance.

defaultItems - Variable in class net.sf.basedb.clients.web.taglib.Select

The project default values.

defaultItems - Variable in class net.sf.basedb.core.data.ProjectData

defaultKeyManagers - Static variable in class net.sf.basedb.util.ssl.SSLUtil2

defaultLogger - Variable in class net.sf.basedb.core.log.db.DbLogManagerFactory

defaultMaxRecent - Static variable in class net.sf.basedb.clients.web.Base

defaultMimeType - Variable in class net.sf.basedb.clients.web.servlet.Download

defaultPlatformFunction - Variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter

defaultPreset - Variable in class net.sf.basedb.core.Presets

defaultPriority - Variable in enum class net.sf.basedb.core.Job.ExecutionTime

defaultProtocolFunction - Variable in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter

defaultProtocolFunction - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

defaultProtocolFunction - Variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter

defaultProtocolFunction - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

defaultPrototolFunction - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter

defaultPrototolFunction - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter

defaultReporterContext - Static variable in class net.sf.basedb.clients.web.ExperimentExplorer

The default context for the reporter search page.

DefaultRequestHandler - Class in net.sf.basedb.clients.jobagent.handlers

This is the default request handler for incoming requests to a job agent.

DefaultRequestHandler(Agent) - Constructor for class net.sf.basedb.clients.jobagent.handlers.DefaultRequestHandler

defaultScale - Static variable in class net.sf.basedb.clients.web.Base

defaultSelects - Variable in class net.sf.basedb.core.DynamicExtraValueQuery

defaultSelects - Variable in class net.sf.basedb.core.DynamicPositionQuery

defaultSelects - Variable in class net.sf.basedb.core.DynamicSpotQuery

defaultSettings - Variable in class net.sf.basedb.core.data.ClientData

defaultSettings - Variable in class net.sf.basedb.core.data.UserData

defaultSeverity - Variable in class net.sf.basedb.util.overview.Validator

defaultSlots - Variable in enum class net.sf.basedb.core.Job.ExecutionTime

defaultSocketFactory - Static variable in class net.sf.basedb.util.ssl.SSLUtil2

defaultSoftwareFunction - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

defaultSoftwareFunction - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

defaultSpotContexts - Static variable in class net.sf.basedb.clients.web.ExperimentExplorer

Stores default context for the spot data list on the view page.

defaultsSection - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

defaultTrustManagers - Static variable in class net.sf.basedb.util.ssl.SSLUtil2

defaultUnit - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo

defaultUnit - Variable in class net.sf.basedb.core.data.AnnotationTypeData

defaultUnitColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

Column mapping parameter for "Default unit".

defaultUnitMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

defaultValue - Variable in class net.sf.basedb.core.data.AnnotationTypeData

defaultValue - Variable in class net.sf.basedb.core.ParameterType

Default value of the parameter.

defaultValue - Variable in class net.sf.basedb.core.PluginParameter

A default value that overrides the default set by the parameter type.

defaultValue - Variable in class net.sf.basedb.core.query.ParameterExpression

defaultValue - Variable in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter

defaultValue - Variable in class net.sf.basedb.plugins.executor.ParameterDefinition

defaultValue - Variable in class net.sf.basedb.util.extensions.debug.StringConverter

defaultValue - Variable in class net.sf.basedb.util.formatter.LookupFormatter

defaultValueColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

Column mapping parameter for "Default value".

defaultValueMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

defaultValues - Variable in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues

defaultVariantFunction - Variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter

defaultWidth - Variable in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet

defaultWidth - Variable in class net.sf.basedb.clients.web.servlet.PlotServlet

deferred - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

definedColumns - Variable in class net.sf.basedb.clients.web.taglib.table.Table

The ID of all defined columns

definedPermissions - Variable in enum class net.sf.basedb.core.Item

DefinedPermissions() - Constructor for class net.sf.basedb.core.Item.DefinedPermissions

defineFilter(Element, Item, String, String, HibernateUtil.FilterConfigurator) - Static method in class net.sf.basedb.core.HibernateUtil

Define a filter for on the given class.

definePackage(String, Manifest) - Method in class net.sf.basedb.util.JarClassLoader

Define the package with the given name using information from a manifest for vendor, title and version.

defultUnit - Variable in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil

delayed - Variable in class net.sf.basedb.core.ItemList

delayed - Variable in class net.sf.basedb.core.Job.JobSignalTransporter

delayedAdd(Listable) - Method in class net.sf.basedb.core.ItemList

DelayedAdditionManager(ItemListData) - Constructor for class net.sf.basedb.core.ItemList.DelayedAdditionManager

DelayedFilterDef(String, Item, String) - Constructor for class net.sf.basedb.core.HibernateUtil.DelayedFilterDef

delayedFilters - Variable in class net.sf.basedb.core.HibernateUtil.FilterConfigurator

delayedRemove(Listable) - Method in class net.sf.basedb.core.ItemList

delayRegistration - Variable in class net.sf.basedb.util.extensions.manager.processor.IgnoreFileProcessor

delayRegistration - Variable in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor

delegateFirst - Variable in class net.sf.basedb.util.JarClassLoader

If we should delegate to the parent class loader first.

DelegatingSignalHandler - Class in net.sf.basedb.core.signal

A signal handler implementation that can delegate to other signal handlers, depending on which signal it receives.

DelegatingSignalHandler() - Constructor for class net.sf.basedb.core.signal.DelegatingSignalHandler

Create a new delegating signal handler.

DelegatingSignalHandler(SignalHandler...) - Constructor for class net.sf.basedb.core.signal.DelegatingSignalHandler

Create a new delegating signal handler and register the given handlers as delegates.

delete - Static variable in class net.sf.basedb.core.Item.DefinedPermissions

delete(int) - Method in class net.sf.basedb.core.BasicBatcher

Delete a data object by id.

delete(int) - Method in class net.sf.basedb.core.FeatureBatcher

Always throws a PermissionDeniedException, since a feature cannot be modifed once it has been created.

delete(int) - Method in class net.sf.basedb.core.RawDataBatcher

Always throws a PermissionDeniedException, since raw data cannot be modifed once it has been created, except if all spots are deleted at the same time.

delete(D) - Method in class net.sf.basedb.core.BasicBatcher

Delete a data object.

delete(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

delete(Object) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

delete(String, int) - Method in class net.sf.basedb.util.StaticCache

Deletes an object from the cache.

delete(String, Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

delete(String, Object) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

delete(DbControl, Item, Set<Integer>) - Static method in class net.sf.basedb.util.RemovableUtil

delete(SessionControl, Collection<? extends Identifiable>, boolean, ProgressReporter) - Static method in class net.sf.basedb.core.Trashcan

Delete items permanently.

DELETE - Enum constant in enum class net.sf.basedb.core.log.ChangeType

DELETE - Enum constant in enum class net.sf.basedb.core.Permission

This permission allows a user delete an item.

DELETE - Enum constant in enum class net.sf.basedb.core.Transactional.Action

The item is an existing item which is beeing deleted.

deleteAll() - Method in class net.sf.basedb.core.FeatureBatcher

Delete all features belonging to this array design.

deleteAll() - Method in class net.sf.basedb.core.RawDataBatcher

Delete all raw data.

deleteAll(SessionControl, ProgressReporter) - Static method in class net.sf.basedb.core.Trashcan

Delete all items in the trashcan of the logged in user.

deleteAllCubeData(short) - Method in class net.sf.basedb.core.VirtualDb

Delete all analysed data for the specified data cube.

deleteAllCubeExtraValueData(short, short, VirtualTable) - Method in class net.sf.basedb.core.VirtualDb

Delete all extra value data for the specified extra value type in the specified data cube.

deleteAllCubeFilterData(short, short) - Method in class net.sf.basedb.core.VirtualDb

Delete all analysed data for the specified filter in the specified data cube.

deleteAllCubeLayerData(short, short) - Method in class net.sf.basedb.core.VirtualDb

Delete all analysed data for the specified layer in the specified data cube.

deleteAnalysedData() - Method in class net.sf.basedb.core.BioAssaySet

Called when a bioassayset is about to be deleted.

deleteAnnotationsForNonExistingProjects() - Method in class net.sf.basedb.core.ProjectSpecificAnnotationsManager

deleteContext(int) - Method in class net.sf.basedb.core.SessionControl

Delete a context.

deleteCount - Variable in class net.sf.basedb.core.BasicBatcher

deleteCurrentContexts(Item, boolean, boolean) - Method in class net.sf.basedb.core.SessionControl

Delete all default contexts for the logged in user.

deleted - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

DELETED - Enum constant in enum class net.sf.basedb.core.AnnotationBatcher.Change

An existing annotation was deleted.

deleteData(Session, BasicData) - Static method in class net.sf.basedb.core.HibernateUtil

Delete a data item from the database.

deletedDefault - Variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager

DeletedFilter - Class in net.sf.basedb.util.extensions.manager.filter

Filter implementation for extension files that allow only deleted files to pass.

DeletedFilter() - Constructor for class net.sf.basedb.util.extensions.manager.filter.DeletedFilter

Create a new filter.

deleteDir(File) - Method in class net.sf.basedb.plugins.Base1PluginExecuter

Deletes all files and sub directories under dir.

deletedPrimary - Variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager

deleteEmptyAnnotationSets(ProgressReporter) - Static method in class net.sf.basedb.core.AnnotationSet

Delete all empty annotation sets.

deleteEmptyAnnotationSets(Session, ProgressReporter) - Static method in class net.sf.basedb.core.AnnotationSet

Delete all empty annotation sets.

deleteEmptyDirectories(File, boolean) - Static method in class net.sf.basedb.util.FileUtil

Deletes all empty subdirectories and, optionally, also the root directory.

deleteFromAnnotations - Variable in class net.sf.basedb.core.AnnotationBatcher

deleteFromParameterValues - Variable in class net.sf.basedb.core.AnnotationBatcher

deleteInheritedAnnotations - Variable in class net.sf.basedb.core.AnnotationBatcher

deleteItem(BasicItem) - Method in class net.sf.basedb.core.DbControl

Schedule an existing item to be deleted from the database.

deleteMode - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

deletePreset(String) - Method in class net.sf.basedb.core.Presets

Delete a named preset.

deleteProducts() - Method in class net.sf.basedb.core.Transformation

Delete all product bioassaysets.

deleteRawData() - Method in class net.sf.basedb.core.RawBioAssay

Delete the raw data that has been added to the database for this raw bioassay.

DeleteResourcesProcessor - Class in net.sf.basedb.util.extensions.manager.processor

A file processor implementation that removes all resources that was previously extracted from a JAR file.

DeleteResourcesProcessor(File, ProcessResults) - Constructor for class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor

Create a new processor.

deleteSnapshotIfModifed - Variable in class net.sf.basedb.core.AnnotationBatcher

deleteSql - Variable in class net.sf.basedb.core.BasicBatcher

deleteStatement - Variable in class net.sf.basedb.core.BasicBatcher

deleteStrayEntries(ProgressReporter) - Static method in class net.sf.basedb.core.ChangeHistory

Delete all history entries that are linking to non-existing items.

deleteStrayLinks(ProgressReporter) - Static method in class net.sf.basedb.core.AnyToAny

Delete all links that are linking to non-existing items.

deleteTempDirectory(File) - Static method in class net.sf.basedb.util.FileUtil

Recursively delete all files and subdirectories within a given directory and the also the given directory itself.

deleteUnusedItemKeys() - Static method in class net.sf.basedb.core.ItemKey

Delete all keys that are currently not used by any item.

deleteUnusedProjectKeys() - Static method in class net.sf.basedb.core.ProjectKey

Delete all keys that are currently not used by any item.

deleteValues - Variable in class net.sf.basedb.core.AnnotationBatcher

DELETION_ORDER - Static variable in enum class net.sf.basedb.core.Item

deletionOrder - Variable in enum class net.sf.basedb.core.Item

delta - Variable in class net.sf.basedb.plugins.LowessNormalization.CallableWorker

deltaMidMax - Variable in class net.sf.basedb.util.ColorGenerator

The difference of the RGB components of the mid and max colors. [0] = red; [1] = green; [2] = blue

deltaMinMid - Variable in class net.sf.basedb.util.ColorGenerator

The difference of the RGB components of the min and mid colors. [0] = red; [1] = green; [2] = blue

deltaParameter - Static variable in class net.sf.basedb.plugins.LowessNormalization

denied - Variable in class net.sf.basedb.clients.web.taglib.Select

If the logged in user was denied access to the current item.

denied - Variable in class net.sf.basedb.core.data.keyring.PluginKeys

denied - Variable in class net.sf.basedb.core.data.PluginPermission

denied - Variable in class net.sf.basedb.core.PluginPermission

DENIED - Enum constant in enum class net.sf.basedb.core.Permission

This permission denies a user access to an item.

DENIED_ANNOTATIONTYPE - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for denied access to an annotation type.

DENIED_ANYTOANY - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for denied access the referenced item in an any-to-any link.

DENIED_ARRAYBATCH - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for denied access to an array batch.

DENIED_ARRAYDESIGN - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for denied access to an array design.

DENIED_ARRAYSLIDE - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for denied access to array slides.

DENIED_BIOPLATE - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for denied access to a bioplate.

DENIED_BIOSOURCE - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for denied access to biosource.

DENIED_DATAFILETYPE - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for denied access to data file types.

DENIED_DERIVEDBIOASSAY - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for denied access to derived bioassay.

DENIED_EXTRACT - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for denied access to extracts.

DENIED_FILE - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for denied access to (data) files.

DENIED_HARDWARE - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for denied access to hardware.

DENIED_KIT - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for denied access to kit.

DENIED_PHYSICALBIOASSAY - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for denied access to physical bioassay.

DENIED_PLATFORM - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for denied access to platform.

DENIED_PROTOCOL - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for denied access to protocols.

DENIED_SAMPLE - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for denied access to samples.

DENIED_SOFTWARE - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for denied access to software.

DENIED_TAG - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for denied access to tags.

DENSITY - Static variable in class net.sf.basedb.core.Quantity

The id for the Quantity object representing density.

deny(Set<Permission>) - Static method in enum class net.sf.basedb.core.Permission

Combine the given permission and convert to the integer deny value.

deny(Permission) - Static method in enum class net.sf.basedb.core.Permission

Convert the given permission to the integer deny value.

deny(Permission...) - Static method in enum class net.sf.basedb.core.Permission

Combine the given permissions and convert to the integer deny value.

DENY_ALL_FILTER - Static variable in class net.sf.basedb.core.QueryRuntimeFilterFactory

DENY_ITEM - Static variable in class net.sf.basedb.core.Keyring

DENY_ROOT_NODE - Static variable in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader

DenyAllFilter() - Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.DenyAllFilter

denyValue - Variable in enum class net.sf.basedb.core.Permission

denyValue() - Method in enum class net.sf.basedb.core.Permission

DeprecationLogger - Class in net.sf.basedb.clients.web.taglib

Utility class for logging use of deprecated taglib attributes.

DeprecationLogger() - Constructor for class net.sf.basedb.clients.web.taglib.DeprecationLogger

depth - Variable in class net.sf.basedb.util.Tree.Entry

DerivedBioAssay - Class in net.sf.basedb.core

DerivedBioAssay(DerivedBioAssayData) - Constructor for class net.sf.basedb.core.DerivedBioAssay

DERIVEDBIOASSAY - Enum constant in enum class net.sf.basedb.core.Item

The item is a DerivedBioAssay.

DerivedBioAssay.FixDerivedBioAssayParentsRecursivelyAction - Class in net.sf.basedb.core

Whenever we modify the parent items to a derived bioassay, we must make sure that the physical bioassays for all child items are synchronized with the same changes.

DerivedBioAssayData - Class in net.sf.basedb.core.data

DerivedBioAssayData() - Constructor for class net.sf.basedb.core.data.DerivedBioAssayData

DerivedBioAssayImporter - Class in net.sf.basedb.plugins.batchimport

Plug-in for importing derived bioassay items in a batch.

DerivedBioAssayImporter() - Constructor for class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

DerivedBioAssayLoader - Class in net.sf.basedb.util.overview.loader

DerivedBioAssayLoader() - Constructor for class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader

derivedBioAssayQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

derivedBioAssays - Variable in class net.sf.basedb.core.data.ExtractData

derivedBioAssays - Variable in class net.sf.basedb.core.data.JobData

derivedBioAssays - Variable in class net.sf.basedb.core.data.PhysicalBioAssayData

DerivedBioAssayToChildDerivedBioAssayTransformer - Class in net.sf.basedb.util.listable

Source item transformer implementation that transform derived bioassay items to child derived bioassays.

DerivedBioAssayToChildDerivedBioAssayTransformer(boolean) - Constructor for class net.sf.basedb.util.listable.DerivedBioAssayToChildDerivedBioAssayTransformer

Create a new derived bioassay to child derived bioassay transformer.

DerivedBioAssayToParentDerivedBioAssayTransformer - Class in net.sf.basedb.util.listable

Source item transformer implementation that transform derived bioassay items to parent derived bioassays.

DerivedBioAssayToParentDerivedBioAssayTransformer(boolean) - Constructor for class net.sf.basedb.util.listable.DerivedBioAssayToParentDerivedBioAssayTransformer

Create a new derived bioassay to parent derived bioassay transformer.

DerivedBioAssayToPhysicalBioAssayTransformer - Class in net.sf.basedb.util.listable

Source item transformer implementation that transform derived bioassay items to physical bioassays.

DerivedBioAssayToPhysicalBioAssayTransformer() - Constructor for class net.sf.basedb.util.listable.DerivedBioAssayToPhysicalBioAssayTransformer

Create a new derived bioassay to physical bioassay transformer.

DerivedBioAssayToRawBioAssayTransformer - Class in net.sf.basedb.util.listable

Source item transformer implementation that transform derived bioassay items to raw bioassays.

DerivedBioAssayToRawBioAssayTransformer() - Constructor for class net.sf.basedb.util.listable.DerivedBioAssayToRawBioAssayTransformer

Create a new derived bioassay to raw bioassay transformer.

DerivedBioAssayToRawBioAssayTransformer(CollectExtracts) - Constructor for class net.sf.basedb.util.listable.DerivedBioAssayToRawBioAssayTransformer

Create a new derived bioassay to raw bioassay transformer that also consider collected parent extracts.

DerivedBioAssayValidator - Class in net.sf.basedb.util.overview.validator

Validator implementation for derived bioassays.

DerivedBioAssayValidator() - Constructor for class net.sf.basedb.util.overview.validator.DerivedBioAssayValidator

desc(Expression) - Static method in class net.sf.basedb.core.query.Orders

Sort the result of a query in descending order by the expression.

DESC - Enum constant in enum class net.sf.basedb.core.ItemContext.SortDirection

Items are sorted in descending order.

descending - Variable in class net.sf.basedb.util.NameableComparator

descending - Variable in class net.sf.basedb.util.ToStringComparator

DescOrder - Class in net.sf.basedb.core.query

Sort the result of a query in descending order by the expression.

DescOrder(Expression) - Constructor for class net.sf.basedb.core.query.DescOrder

description - Variable in class net.sf.basedb.clients.jobagent.Agent

description - Variable in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean

description - Variable in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory

description - Variable in class net.sf.basedb.clients.web.extensions.startpage.StartPageBean

description - Variable in class net.sf.basedb.clients.web.taglib.table.TableColumn

description - Variable in class net.sf.basedb.core.authentication.ExtraUserInformation

description - Variable in class net.sf.basedb.core.data.AnyToAnyData

description - Variable in class net.sf.basedb.core.data.BioAssayData

description - Variable in class net.sf.basedb.core.data.BioAssaySetData

description - Variable in class net.sf.basedb.core.data.BioPlateEventTypeData

description - Variable in class net.sf.basedb.core.data.BioPlateTypeData

description - Variable in class net.sf.basedb.core.data.CommonData

description - Variable in class net.sf.basedb.core.data.DataFileTypeData

description - Variable in class net.sf.basedb.core.data.ExtraValueTypeData

description - Variable in class net.sf.basedb.core.data.GroupData

description - Variable in class net.sf.basedb.core.data.HelpData

description - Variable in class net.sf.basedb.core.data.ItemListSyncFilterData

description - Variable in class net.sf.basedb.core.data.ItemSubtypeData

description - Variable in class net.sf.basedb.core.data.MessageData

description - Variable in class net.sf.basedb.core.data.MimeTypeData

description - Variable in class net.sf.basedb.core.data.NewsData

description - Variable in class net.sf.basedb.core.data.ParameterValueData

description - Variable in class net.sf.basedb.core.data.PlateEventTypeData

description - Variable in class net.sf.basedb.core.data.PlateGeometryData

description - Variable in class net.sf.basedb.core.data.PlatformData

description - Variable in class net.sf.basedb.core.data.PlatformVariantData

description - Variable in class net.sf.basedb.core.data.PluginDefinitionData

description - Variable in class net.sf.basedb.core.data.PluginTypeData

description - Variable in class net.sf.basedb.core.data.ProjectData

description - Variable in class net.sf.basedb.core.data.QuantityData

description - Variable in class net.sf.basedb.core.data.QuotaData

description - Variable in class net.sf.basedb.core.data.QuotaTypeData

description - Variable in class net.sf.basedb.core.data.ReporterClonePropertyData

description - Variable in class net.sf.basedb.core.data.ReporterData

description - Variable in class net.sf.basedb.core.data.ReporterTypeData

description - Variable in class net.sf.basedb.core.data.RoleData

description - Variable in class net.sf.basedb.core.data.RoleKeyData

description - Variable in class net.sf.basedb.core.data.RootRawBioAssayData

description - Variable in class net.sf.basedb.core.data.TransformationData

description - Variable in class net.sf.basedb.core.data.UnitData

description - Variable in class net.sf.basedb.core.data.UserData

description - Variable in class net.sf.basedb.core.data.UserDeviceData

description - Variable in class net.sf.basedb.core.ExtendedProperty

description - Variable in class net.sf.basedb.core.IntensityFormula

description - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba

description - Variable in class net.sf.basedb.core.ParameterInfo

description - Variable in class net.sf.basedb.core.plugin.AboutImpl

description - Variable in class net.sf.basedb.core.PluginParameter

A longer help text explaining what the particular parameter is needed for.

description - Variable in class net.sf.basedb.core.RawDataType

description - Variable in class net.sf.basedb.core.RequestInformation

description - Variable in class net.sf.basedb.core.signal.Signal

description - Variable in class net.sf.basedb.plugins.executor.ParameterDefinition

description - Variable in class net.sf.basedb.util.extensions.AboutBean

description - Variable in class net.sf.basedb.util.extensions.ExtensionPointBean

description - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredAbout

description - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint

description - Variable in class net.sf.basedb.util.overview.Validator

description - Variable in class net.sf.basedb.util.uri.http.HttpConnectionManagerFactory

DESCRIPTION - Static variable in class net.sf.basedb.core.ClonableProperty

The property name of the "static" property ReporterData.getDescription()

descriptionColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

descriptionColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

descriptionMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

descriptionMapper - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

descriptionMapper - Variable in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter

descriptionMapper - Variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter

descriptionMapper - Variable in class net.sf.basedb.plugins.batchimport.ArraySlideImporter

descriptionMapper - Variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter

descriptionMapper - Variable in class net.sf.basedb.plugins.batchimport.BioSourceImporter

descriptionMapper - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

descriptionMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter

descriptionMapper - Variable in class net.sf.basedb.plugins.batchimport.FileImporter

descriptionMapper - Variable in class net.sf.basedb.plugins.batchimport.KitImporter

descriptionMapper - Variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter

descriptionMapper - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

descriptionMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter

descriptionMapper - Variable in class net.sf.basedb.plugins.batchimport.TagImporter

descriptionMapper - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

descriptionParameter - Static variable in class net.sf.basedb.plugins.PlateMappingImporter

descriptionType - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

A parameter type for description parameters.

descriptor - Variable in class net.sf.basedb.util.overview.Failure

deserializeObject(ObjectInputStream) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

design - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter

design - Variable in class net.sf.basedb.util.affymetrix.CdfValidationAction

design - Variable in class net.sf.basedb.util.gtf.GtfValidationAction

designQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

destColumnMapper - Variable in class net.sf.basedb.plugins.PlateMappingImporter

destinationCount - Variable in class net.sf.basedb.core.data.PlateMappingData

destinationGeometry - Variable in class net.sf.basedb.core.data.PlateMappingData

destinationIndex - Variable in class net.sf.basedb.core.data.PlateData

destPlateMapper - Variable in class net.sf.basedb.plugins.PlateMappingImporter

destRowMapper - Variable in class net.sf.basedb.plugins.PlateMappingImporter

destroy() - Method in class net.sf.basedb.clients.web.servlet.CacheControlFilter

destroy() - Method in class net.sf.basedb.clients.web.servlet.CharacterEncodingFilter

destroy() - Method in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter

destroy() - Method in class net.sf.basedb.clients.web.servlet.ImageRemapFilter

destroyed - Variable in class net.sf.basedb.core.data.ArraySlideData

destroyed - Variable in class net.sf.basedb.core.data.BioPlateData

destroyed - Variable in class net.sf.basedb.core.data.PlateData

destroyedColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.ArraySlideImporter

destroyedMapper - Variable in class net.sf.basedb.plugins.batchimport.ArraySlideImporter

detach(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

DetachedItemException - Exception in net.sf.basedb.core

This exception is thrown when trying to use an item that has been detached from the DbControl that manages it.

DetachedItemException(String) - Constructor for exception net.sf.basedb.core.DetachedItemException

Creates a new DetachedItemException.

detachItem(BasicItem) - Method in class net.sf.basedb.core.DbControl

Detach an item from this DbControl.

detail - Variable in exception net.sf.basedb.clients.web.WebException

A more detailed description of the error message.

detailedProperties - Variable in class net.sf.basedb.core.log.db.AnnotationSetLogger

detailedProperties - Variable in class net.sf.basedb.core.log.db.BioMaterialEventLogger

detailedProperties - Variable in class net.sf.basedb.core.log.db.DbLogManagerFactory

detailedProperties - Variable in class net.sf.basedb.core.log.db.DefaultEntityLogger

detailedProperties - Variable in class net.sf.basedb.core.log.db.ManualEntryLogger

detailedProperties - Variable in class net.sf.basedb.core.log.db.PlateEventLogger

details - Variable in class net.sf.basedb.core.data.ChangeHistoryData

details - Variable in class net.sf.basedb.core.data.PlateMappingData

details - Variable in class net.sf.basedb.core.log.LoggingInterceptor.LogDetails

detector - Variable in class net.sf.basedb.core.File.CharsetTesterThread

determineProperBooleanType(int, Object, Type) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

determineProperBooleanType(String, Object, Type) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

device - Variable in class net.sf.basedb.core.data.SessionData

device - Variable in class net.sf.basedb.core.SessionControl.UnverifiedDeviceInfo

deviceId - Variable in class net.sf.basedb.core.SessionControl.LoginInfo

The id of the UserDevice in use.

deviceName - Variable in class net.sf.basedb.core.SessionControl.LoginInfo

DeviceNotVerifiedException - Exception in net.sf.basedb.core

This exception can be thrown when a user is trying to login from a device that has not been verified.

DeviceNotVerifiedException() - Constructor for exception net.sf.basedb.core.DeviceNotVerifiedException

devices - Variable in class net.sf.basedb.core.data.ClientData

devices - Variable in class net.sf.basedb.core.data.UserData

deviceToken - Variable in class net.sf.basedb.core.authentication.LoginRequest

dialect - Variable in class net.sf.basedb.core.AnnotationBatcher

dialect - Variable in class net.sf.basedb.core.dbengine.TableInfo

dialect - Variable in class net.sf.basedb.core.hibernate.DbIndexWork

dialect - Variable in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget

dialect - Variable in class net.sf.basedb.core.hibernate.SchemaGenerator

dialect - Static variable in class net.sf.basedb.core.HibernateUtil

The Hibernate database dialect in use.

dialect - Variable in class net.sf.basedb.core.MigrateRbaToDba

dialectDom - Static variable in class net.sf.basedb.core.PredefinedQuery

Holds the XML document containing the dialect-specific queries.

dialectQueryFile - Static variable in class net.sf.basedb.core.PredefinedQuery

The path to the query file with dialect-specific queries.

Diff3 - Class in net.sf.basedb.util

This class is helpful when a client application needs to implement long-running transactions and still be able to update items with as few clashes as possible.

Diff3(BasicItem, BasicItem) - Constructor for class net.sf.basedb.util.Diff3

Create a new Diff3 object to compare properties of the oldItem and newItem.

DIFFERENT_TAG - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if the parent to a tagged extract has a different tag.

dir - Variable in class net.sf.basedb.util.bfs.BaseInputStreamLocator

dir - Variable in class net.sf.basedb.util.bfs.DiskInputStreamLocator

dir - Variable in class net.sf.basedb.util.bfs.GenericBaseDataWriterFactory

dir - Variable in class net.sf.basedb.util.bfs.GenericDiskDataWriterFactory

dir - Variable in class net.sf.basedb.util.bfs.GenericExtraFileImporter

direction - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

direction - Variable in class net.sf.basedb.util.overview.cache.DirectionalCacheKey

direction - Variable in class net.sf.basedb.util.overview.Node

DirectionalCacheKey - Class in net.sf.basedb.util.overview.cache

Cache key implementation that bundles another cache key with a node direction.

DirectionalCacheKey(Object, ChildNodeDirection) - Constructor for class net.sf.basedb.util.overview.cache.DirectionalCacheKey

directionRaw - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

directories - Variable in class net.sf.basedb.core.Path

The directory part of the path.

directories - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsManager

directory - Variable in class net.sf.basedb.core.data.ExperimentData

directory - Variable in class net.sf.basedb.core.data.FileData

directory - Variable in class net.sf.basedb.core.Migration

Directory - Class in net.sf.basedb.core

This is used to represent directory items.

Directory(DirectoryData) - Constructor for class net.sf.basedb.core.Directory

Creates a new directory item from the given data.

DIRECTORY - Enum constant in enum class net.sf.basedb.core.Item

The item is a Directory.

DIRECTORY - Enum constant in enum class net.sf.basedb.core.Path.Type

The path is a path to a Directory.

DIRECTORY_CACHE - Static variable in class net.sf.basedb.core.Directory

DirectoryData - Class in net.sf.basedb.core.data

This class holds information about directories.

DirectoryData() - Constructor for class net.sf.basedb.core.data.DirectoryData

directoryGui - Static variable in class net.sf.basedb.plugins.PackedFileExporter

directoryPattern - Variable in class net.sf.basedb.util.RegexpFileFilter

dirty - Variable in class net.sf.basedb.core.log.EntityDetails

disableAll() - Method in class net.sf.basedb.core.QueryRuntimeFilterManager

Disable all filters.

disableATPermissionCheck - Variable in class net.sf.basedb.core.Annotation

disableATPermissionCheck() - Method in class net.sf.basedb.core.Annotation

disableChangeLogColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

Column mapping parameter for "Disabled history log" flag.

disableChangeLogMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

disabled - Variable in class net.sf.basedb.clients.web.taglib.Button

If the button should be enabled or not.

disabled - Variable in class net.sf.basedb.clients.web.taglib.Select

If the selection list should be enabled or not.

disabled - Variable in class net.sf.basedb.clients.web.taglib.table.Button

IF the button is disabled or not.

disabled - Variable in class net.sf.basedb.core.data.ItemListSyncFilterData

disabled - Variable in class net.sf.basedb.core.data.PluginConfigurationData

disabled - Variable in class net.sf.basedb.core.data.PluginDefinitionData

disabled - Variable in class net.sf.basedb.core.data.UserData

disabled - Variable in class net.sf.basedb.core.snapshot.DisabledInheritanceFilter

disabled - Variable in class net.sf.basedb.util.extensions.debug.BeanActionFactory

disabled - Variable in class net.sf.basedb.util.extensions.debug.ProxyActionFactory

disabled - Variable in class net.sf.basedb.util.extensions.xml.PluginInfo

disabled - Variable in class net.sf.basedb.util.overview.validator.BasicItemNodeValidatorFactory

disabled - Variable in class net.sf.basedb.util.StaticCache

disabledClazz - Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

disabledClazz - Variable in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

disableDeviceVerification() - Method in class net.sf.basedb.core.User

Disable device verification.

disabledExtensionPoints - Variable in class net.sf.basedb.util.extensions.manager.Settings

disabledExtensions - Variable in class net.sf.basedb.util.extensions.manager.Settings

disabledIcon - Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

disabledIcon - Variable in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

disabledInheritanceFilter - Variable in class net.sf.basedb.core.snapshot.SnapshotManager

DisabledInheritanceFilter - Class in net.sf.basedb.core.snapshot

Filter implementation that filters away annotations that have an annotation type with inheritance disabled.

DisabledInheritanceFilter(DbControl) - Constructor for class net.sf.basedb.core.snapshot.DisabledInheritanceFilter

Create a new filter.

DisabledInheritanceFilter(DisabledInheritanceFilter) - Constructor for class net.sf.basedb.core.snapshot.DisabledInheritanceFilter

Create a clone of another filter instance.

disabledStyle - Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

disabledStyle - Variable in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

disabledTitle - Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

disabledTitle - Variable in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

disabledTooltip - Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

disabledTooltip - Variable in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

disableExtensions - Variable in class net.sf.basedb.core.Application.StartupOptions

disableExtensions(boolean) - Method in class net.sf.basedb.core.Application.StartupOptions

Set to TRUE to disable loading external extensions.

disableFetchProfile(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

disableFilter(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

disableFilter(String) - Method in class net.sf.basedb.core.QueryRuntimeFilterManager

Disable a filter.

disableFilter(Session, String) - Static method in class net.sf.basedb.core.HibernateUtil

Disable the filter with the given name.

disableFilters(DbControl) - Method in class net.sf.basedb.core.AbstractEntityQuery

Disable all enabled runtime query filters for the query.

disableForItem(Item) - Method in class net.sf.basedb.core.AnnotationType

Disable this annotation type to be used for items of the specified type.

disableInheritance - Variable in class net.sf.basedb.core.data.AnnotationTypeData

disableInheritanceColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

Column mapping parameter for "Disable inheritance" flag.

disableInheritanceMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

disableInProject - Variable in class net.sf.basedb.clients.web.taglib.table.PresetSelector

If the 'in project' option should be included in the preset selector or not.

disableInternalJobQueue - Variable in class net.sf.basedb.core.Application.StartupOptions

disableInternalJobQueue(boolean) - Method in class net.sf.basedb.core.Application.StartupOptions

Set to TRUE to disable the internal job queue.

disableLogOfValues - Variable in class net.sf.basedb.core.data.AnnotationTypeData

disableManualMembers - Variable in class net.sf.basedb.core.data.ItemListData

disableOthers - Variable in class net.sf.basedb.clients.web.taglib.table.PresetSelector

If the 'owned by others' option should be included in the preset selector or not.

disableOverflowCheck - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

disableOverflowCheck - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

disableOverflowCheck - Variable in class net.sf.basedb.clients.web.taglib.table.Cell

disableOwnedBy - Variable in class net.sf.basedb.clients.web.taglib.table.PresetSelector

If the 'owned by me' option should be included in the preset selector or not.

DisablePluginsProcessor - Class in net.sf.basedb.util.extensions.manager.processor

File processor implementation that disables plug-ins.

DisablePluginsProcessor(DbControl, ProcessResults) - Constructor for class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor

Create a new processor.

disableRawJoinOnMergedData - Variable in class net.sf.basedb.core.DynamicSpotQuery

disableRemoved - Variable in class net.sf.basedb.clients.web.taglib.table.PresetSelector

If the 'removed' option should be included in the preset selector or not.

disableSharedTo - Variable in class net.sf.basedb.clients.web.taglib.table.PresetSelector

If the 'shared to me' option should be included in the preset selector or not.

disableSyncFilters - Variable in class net.sf.basedb.core.data.ItemListData

DisallowedValueException - Exception in net.sf.basedb.core

Exception that is thrown when a value is not found among a set of allowed values, for example, when setting an annotation value.

DisallowedValueException() - Constructor for exception net.sf.basedb.core.DisallowedValueException

Create a new DisallowedValueException object.

DisallowedValueException(String) - Constructor for exception net.sf.basedb.core.DisallowedValueException

Create a new DisallowedValueException exception.

DisallowedValueException(String, Object) - Constructor for exception net.sf.basedb.core.DisallowedValueException

Create a new DisallowedValueException object.

disconnect() - Method in class net.sf.basedb.core.DbControl

Deprecated.

In 3.12. Applications should use separate DbControl instead.

disconnect() - Method in class net.sf.basedb.core.hibernate.SessionWrapper

discriminators - Variable in class net.sf.basedb.core.AnnotationBatcher

DiskConsumable - Interface in net.sf.basedb.core

This interface is implemented by items that can use a lot of disk space.

DiskConsumableData - Interface in net.sf.basedb.core.data

A diskconsumable item is an item that occupies a lot of diskspace and should be controlled by the quota system.

diskConsumableItems - Static variable in class net.sf.basedb.core.Metadata

DiskFileWrapper - Class in net.sf.basedb.util.importer

File wrapper implementation for files that are located on the local disk.

DiskFileWrapper(File) - Constructor for class net.sf.basedb.util.importer.DiskFileWrapper

DiskInputStreamLocator - Class in net.sf.basedb.util.bfs

Input stream locator implementation that works with files on the local file system.

DiskInputStreamLocator(File) - Constructor for class net.sf.basedb.util.bfs.DiskInputStreamLocator

Create a new input stream locator.

diskUsage - Variable in class net.sf.basedb.core.data.ExperimentData

diskUsage - Variable in class net.sf.basedb.core.data.FileData

diskUsage - Variable in class net.sf.basedb.core.data.RawBioAssayData

diskUsage - Variable in class net.sf.basedb.core.DiskUsageStatistics.Summary

DiskUsage - Class in net.sf.basedb.core

This class is used to represent the disk usage of DiskConsumable items.

DiskUsage(DiskUsageData) - Constructor for class net.sf.basedb.core.DiskUsage

Create a new DiskUsage item.

DISKUSAGE - Enum constant in enum class net.sf.basedb.core.Item

The item is a DiskUsage.

DiskUsageData - Class in net.sf.basedb.core.data

This class holds information about a users and/or groups disk usage.

DiskUsageData() - Constructor for class net.sf.basedb.core.data.DiskUsageData

Creates a new DiskUsageData.

DiskUsageStatistics - Class in net.sf.basedb.core

Get disk usage statistics for the BASE server.

DiskUsageStatistics(DbControl) - Constructor for class net.sf.basedb.core.DiskUsageStatistics

Create a new disk usage statistics object.

DiskUsageStatistics.Summary - Class in net.sf.basedb.core

Holds summary disk usage information for the total disk usage or for a specific user or group.

display(int, String) - Method in class net.sf.basedb.core.Job.ProgressReporterImpl

display(int, String) - Method in interface net.sf.basedb.core.ProgressReporter

Display a progress message.

display(int, String) - Method in class net.sf.basedb.core.signal.ProgressReporterSignalHandler

display(int, String) - Method in class net.sf.basedb.core.SimpleProgressReporter

display(int, String) - Method in class net.sf.basedb.util.ChainedProgressReporter

display(int, String) - Method in class net.sf.basedb.util.ConsoleProgressReporter

display(int, String) - Method in class net.sf.basedb.util.GeoLocation.ResponseFilter

display(int, String) - Method in class net.sf.basedb.util.TransferRateProgressReporter

Forward the call to the parent if one exists.

displayAbsolute(long, String) - Method in interface net.sf.basedb.core.AbsoluteProgressReporter

Display a progress message.

displayAbsolute(long, String) - Method in class net.sf.basedb.core.SimpleAbsoluteProgressReporter

displayAbsolute(long, String) - Method in class net.sf.basedb.util.GeoLocation.ResponseFilter

displayAbsolute(long, String) - Method in class net.sf.basedb.util.TransferRateProgressReporter

Forward the call to the parent if one exists.

displayName - Variable in class net.sf.basedb.clients.web.extensions.login.LoginFormBean

displaySymbol - Variable in class net.sf.basedb.core.data.UnitData

displayValue - Variable in enum class net.sf.basedb.core.BioMaterialEvent.Type

displayValue - Variable in enum class net.sf.basedb.core.BioWell.LockMode

displayValue - Variable in enum class net.sf.basedb.core.FeatureIdentificationMethod

Returned by the toString method.

displayValue - Variable in enum class net.sf.basedb.core.Formula.AverageMethod

displayValue - Variable in enum class net.sf.basedb.core.Formula.Parser

displayValue - Variable in enum class net.sf.basedb.core.Formula.Type

displayValue - Variable in enum class net.sf.basedb.core.IntensityTransform

Returned by the toString method.

displayValue - Variable in enum class net.sf.basedb.core.Item

displayValue - Variable in enum class net.sf.basedb.core.ItemContext.SortDirection

The string value of this direction.

displayValue - Variable in enum class net.sf.basedb.core.Job.ExecutionTime

displayValue - Variable in enum class net.sf.basedb.core.Job.Status

displayValue - Variable in enum class net.sf.basedb.core.Job.Type

displayValue - Variable in enum class net.sf.basedb.core.Location

Returned by the toString method.

displayValue - Variable in enum class net.sf.basedb.core.Permission

displayValue - Variable in enum class net.sf.basedb.core.plugin.Plugin.MainType

displayValue - Variable in enum class net.sf.basedb.core.Type

displayValue - Variable in enum class net.sf.basedb.util.overview.Severity

distinct - Variable in class net.sf.basedb.core.AbstractQuery

If the query should only return the same item once or not.

distinct - Variable in class net.sf.basedb.core.query.CountExpression

divide(Expression, Expression) - Static method in class net.sf.basedb.core.query.Expressions

Divide one expression by another: new expression = e1 / e2.

DivideConverter - Class in net.sf.basedb.util.jep.convert

Convert Divide function to a Query API Expression.

DivideConverter() - Constructor for class net.sf.basedb.util.jep.convert.DivideConverter

DivideExpression - Class in net.sf.basedb.core.query

Divide one expression by another: e1 / e2.

DivideExpression(Expression, Expression) - Constructor for class net.sf.basedb.core.query.DivideExpression

doAfterBody() - Method in class net.sf.basedb.clients.web.taglib.table.ExtensionCells

doCatch(Throwable) - Method in class net.sf.basedb.clients.web.taglib.ExceptionCatcher

doCatch(Throwable) - Method in class net.sf.basedb.clients.web.taglib.table.Cell

doctype - Variable in class net.sf.basedb.clients.web.taglib.Page

The <!

doEndTag() - Method in class net.sf.basedb.clients.web.taglib.Body

doEndTag() - Method in class net.sf.basedb.clients.web.taglib.ButtonGroup

doEndTag() - Method in class net.sf.basedb.clients.web.taglib.ExceptionCatcher

doEndTag() - Method in class net.sf.basedb.clients.web.taglib.Head

doEndTag() - Method in class net.sf.basedb.clients.web.taglib.HideableSection

doEndTag() - Method in class net.sf.basedb.clients.web.taglib.Icon

doEndTag() - Method in class net.sf.basedb.clients.web.taglib.menu.Menu

doEndTag() - Method in class net.sf.basedb.clients.web.taglib.Page

doEndTag() - Method in class net.sf.basedb.clients.web.taglib.path.Path

doEndTag() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab

doEndTag() - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl

doEndTag() - Method in class net.sf.basedb.clients.web.taglib.table.Cell

doEndTag() - Method in class net.sf.basedb.clients.web.taglib.table.Data

doEndTag() - Method in class net.sf.basedb.clients.web.taglib.table.Form

doEndTag() - Method in class net.sf.basedb.clients.web.taglib.table.Header

doEndTag() - Method in class net.sf.basedb.clients.web.taglib.table.HeaderRow

doEndTag() - Method in class net.sf.basedb.clients.web.taglib.table.Headers

doEndTag() - Method in class net.sf.basedb.clients.web.taglib.table.Label

doEndTag() - Method in class net.sf.basedb.clients.web.taglib.table.Navigator

doEndTag() - Method in class net.sf.basedb.clients.web.taglib.table.Panel

doEndTag() - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector

doEndTag() - Method in class net.sf.basedb.clients.web.taglib.table.Row

doEndTag() - Method in class net.sf.basedb.clients.web.taglib.table.Rows

doEndTag() - Method in class net.sf.basedb.clients.web.taglib.table.Table

doEndTag() - Method in class net.sf.basedb.clients.web.taglib.table.Toolbar

doExport() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

Run the export.

doExport(Connection) - Method in class net.sf.basedb.core.Migration

Perform the export.

doExport(ExportOutputStream, ProgressReporter) - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin

Implements immediate downloading.

doExport(ExportOutputStream, ProgressReporter) - Method in interface net.sf.basedb.core.plugin.ImmediateDownloadExporter

Perform the export.

doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class net.sf.basedb.clients.web.servlet.CacheControlFilter

doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class net.sf.basedb.clients.web.servlet.CharacterEncodingFilter

doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter

doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class net.sf.basedb.clients.web.servlet.ImageRemapFilter

doFinally() - Method in class net.sf.basedb.clients.web.taglib.ExceptionCatcher

doFinally() - Method in class net.sf.basedb.clients.web.taglib.table.Cell

doGet(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.CompileAll

doGet(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.Download

doGet(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet

doGet(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.ExtensionsServlet

doGet(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.PlotServlet

doGet(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.RssNewsFeed

doGet(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.Upload

doImport() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter

Start the import.

doImport() - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter

Start the import.

doImport(InputStream, ProgressReporter) - Method in interface net.sf.basedb.core.plugin.AutoDetectingImporter

Import the data from the given InputStream.

doImport(InputStream, ProgressReporter) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

doImport(InputStream, ProgressReporter) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter

doImport(InputStream, ProgressReporter) - Method in class net.sf.basedb.plugins.CdfFileReporterImporter

doImport(InputStream, ProgressReporter) - Method in class net.sf.basedb.plugins.HelpImporter

doImport(InputStream, ProgressReporter) - Method in class net.sf.basedb.plugins.PluginConfigurationImporter

doImport(Connection) - Method in class net.sf.basedb.core.Migration

Perform the import.

doInsert(RawData, String, String, boolean) - Method in class net.sf.basedb.core.RawDataBatcher

Do the actual insert.

domainRange - Variable in class net.sf.basedb.util.plot.HistogramPlot

done() - Method in class net.sf.basedb.core.plugin.AbstractPlugin

Clears the variables set by the init method.

done() - Method in interface net.sf.basedb.core.plugin.Plugin

This method is called when the core is finished with the plugin object.

done() - Method in class net.sf.basedb.core.PluginRequest

Aborts the execution of the plugin.

done(ExtensionsManager) - Method in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor

done(ExtensionsManager) - Method in class net.sf.basedb.clients.web.extensions.UninstalledFileProcessor

done(ExtensionsManager) - Method in interface net.sf.basedb.util.extensions.manager.ExtensionsFileProcessor

Called by the extensions manager after a successful completion of the processing.

done(ExtensionsManager) - Method in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor

done(ExtensionsManager) - Method in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor

done(ExtensionsManager) - Method in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor

done(ExtensionsManager) - Method in class net.sf.basedb.util.extensions.manager.processor.IgnoreFileProcessor

done(ExtensionsManager) - Method in class net.sf.basedb.util.extensions.manager.processor.MarkAsProcessedProcessor

done(ExtensionsManager) - Method in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor

done(ExtensionsManager) - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor

done(ExtensionsManager) - Method in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor

done(ExtensionsManager) - Method in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor

done(ExtensionsManager, Throwable) - Method in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor

done(ExtensionsManager, Throwable) - Method in class net.sf.basedb.clients.web.extensions.UninstalledFileProcessor

done(ExtensionsManager, Throwable) - Method in interface net.sf.basedb.util.extensions.manager.ExtensionsFileProcessor

Called by the extensions manager if an exception was thrown by the processor.

done(ExtensionsManager, Throwable) - Method in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor

done(ExtensionsManager, Throwable) - Method in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor

done(ExtensionsManager, Throwable) - Method in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor

done(ExtensionsManager, Throwable) - Method in class net.sf.basedb.util.extensions.manager.processor.IgnoreFileProcessor

done(ExtensionsManager, Throwable) - Method in class net.sf.basedb.util.extensions.manager.processor.MarkAsProcessedProcessor

done(ExtensionsManager, Throwable) - Method in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor

done(ExtensionsManager, Throwable) - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor

done(ExtensionsManager, Throwable) - Method in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor

done(ExtensionsManager, Throwable) - Method in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor

DONE - Enum constant in enum class net.sf.basedb.core.Job.Status

The job has finished successfully.

DONE - Enum constant in enum class net.sf.basedb.core.plugin.Response.Status

doneError(String) - Method in class net.sf.basedb.core.Job

Register the job as completed with an error.

doneError(String, Collection<? extends Throwable>) - Method in class net.sf.basedb.core.Job

Register the job as completed with an error.

doneError(String, Collection<? extends Throwable>, Date) - Method in class net.sf.basedb.core.Job

Register the job as completed with an error.

doneOk(String) - Method in class net.sf.basedb.core.Job

Register the job as successfully completed.

doneOk(String, Date) - Method in class net.sf.basedb.core.Job

Register the job as successfully completed.

doneWithItem(DbControl, I, int) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Called when the importer is finished with an item.

doneWithItem(DbControl, ArrayDesign, int) - Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter

Validate data files if they have been set.

doneWithItem(DbControl, DerivedBioAssay, int) - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

Validate data files if they have been set.

doneWithItem(DbControl, RawBioAssay, int) - Method in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

Validate data files if they have been set.

doPost(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.CompileAll

doPost(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyReportServlet

doPost(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.Download

doPost(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.ExtensionsServlet

doPost(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.PlotServlet

Forwards requests to PlotServlet.doGet(HttpServletRequest, HttpServletResponse)

doPost(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.Upload

doRecursively(DbControl, Directory, Filter<? super Directory>, Filter<? super File>) - Static method in class net.sf.basedb.util.FileUtil

Do something recursively to all files and sub-directories in specified root directory.

doReturningWork(ReturningWork<T>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

doReturningWork(Session, ReturningWork<R>) - Static method in class net.sf.basedb.core.HibernateUtil

Execute some arbitrary JDBC code using the same database connection as the Hibernate session.

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.Body

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.Button

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.ButtonGroup

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.extensions.Render

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.extensions.Scripts

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.extensions.Stylesheets

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.Head

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.Help

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.HideableSection

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.Icon

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.Input

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.menu.Menu

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.menu.Menuseparator

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.Page

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.path.Path

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.path.PathElement

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.PropertyValue

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.Select

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.SubtypeSelector

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.Button

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.Cell

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.CellValue

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnHeaders

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnSubtitles

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.Data

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.ExtensionCells

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.Form

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.Header

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.HeaderRow

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.Headers

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.Hidden

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.Label

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.Panel

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.PropertyFilter

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.Row

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.Rows

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.Table

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.Toolbar

doStartTag() - Method in class net.sf.basedb.clients.web.taglib.Zoom

DOUBLE - Enum constant in enum class net.sf.basedb.core.Type

Double type.

DOUBLE - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper

DOUBLE_QUOTE - Static variable in class net.sf.basedb.clients.web.util.HTML

DoubleParameterType - Class in net.sf.basedb.core

This class represent a parameter type that is a double.

DoubleParameterType() - Constructor for class net.sf.basedb.core.DoubleParameterType

Create a new double parameter type, without any limits and allowing null values.

DoubleParameterType(Double, Double, Double, boolean) - Constructor for class net.sf.basedb.core.DoubleParameterType

Create a new double parameter type.

DoubleParameterType(Double, Double, Double, boolean, int, int, int, List<Double>) - Constructor for class net.sf.basedb.core.DoubleParameterType

Create a new double parameter type with a list of allowed values.

DoubleParameterValueData - Class in net.sf.basedb.core.data

Double parameter value.

DoubleParameterValueData() - Constructor for class net.sf.basedb.core.data.DoubleParameterValueData

DoubleParameterValueData(Double...) - Constructor for class net.sf.basedb.core.data.DoubleParameterValueData

doubleValues - Variable in class net.sf.basedb.util.formatter.NumberFormatter

DoubleWriter - Class in net.sf.basedb.core.migrate

Database-independent writer implementation that writes double values from a result set.

DoubleWriter(ResultSet, int, Writer, char[]) - Constructor for class net.sf.basedb.core.migrate.DoubleWriter

doUpload(OutputStream, UploadedFile) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload

Upload a single file section to the specified output stream

download - Variable in class net.sf.basedb.clients.web.servlet.Download

download(OutputStream, long) - Method in class net.sf.basedb.core.File

Download the physical file for this file item.

Download - Class in net.sf.basedb.clients.web.servlet

Download() - Constructor for class net.sf.basedb.clients.web.servlet.Download

DOWNLOAD - Enum constant in enum class net.sf.basedb.core.log.ChangeType

DOWNLOAD_IMMEDIATELY - Enum constant in enum class net.sf.basedb.core.plugin.Response.Status

downloadable - Variable in enum class net.sf.basedb.core.Location

If the file can be downloaded from this location.

downloadCache - Variable in class net.sf.basedb.core.File

Files that are EXTERNAL are cached locally per transaction

downloadImmediately(ExportOutputStream, ProgressReporter) - Method in class net.sf.basedb.core.PluginResponse

doWork(Work) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

doWork(Session, Work) - Static method in class net.sf.basedb.core.HibernateUtil

Execute some arbitrary JDBC code using the same database connection as the Hibernate session.

dragColumns - Variable in class net.sf.basedb.clients.web.taglib.table.Table

dropAllTables() - Method in class net.sf.basedb.core.VirtualDb

Drop all real database tables in this virtual database.

dropClonedReporters() - Method in class net.sf.basedb.core.ReporterCloneBatcher

Drop the cloned reporter information from the dynamic database.

dropColumn(Session, String, String, ProgressReporter) - Static method in class net.sf.basedb.core.Update

DropColumnChange(String, String) - Constructor for class net.sf.basedb.core.Update.DropColumnChange

dropConstraintsBeforeImport - Variable in class net.sf.basedb.core.Migration

dropDynamicTable(String) - Static method in class net.sf.basedb.core.HibernateUtil

DropDynamicTableAction - Class in net.sf.basedb.core

Transactional action that can drop a table from the dynamic database after a successful commit and/or rollback.

DropDynamicTableAction(String, boolean, boolean) - Constructor for class net.sf.basedb.core.DropDynamicTableAction

Create a new drop table action.

dropForeignKeysUsedInIndex() - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine

dropForeignKeysUsedInIndex() - Method in interface net.sf.basedb.core.dbengine.DbEngine

When dropping an index, must foreign keys that uses the same columns also be dropped (before dropping the index)?

dropForeignKeysUsedInIndex() - Method in class net.sf.basedb.core.dbengine.MySQLEngine

dropIndex(Session, boolean, String, String...) - Static method in class net.sf.basedb.core.Update

dropIndexes - Variable in class net.sf.basedb.core.hibernate.DbIndexWork

dropNotNullConstraint(Session, String, String, String) - Static method in class net.sf.basedb.core.Update

dropPrimaryKeyBeforeImport - Variable in class net.sf.basedb.core.Migration

dropTable(Session, String) - Static method in class net.sf.basedb.core.Update

dropVirtualTable(VirtualDb, VirtualTable) - Static method in class net.sf.basedb.core.HibernateUtil

Drop a table in the dynamic database.

DRY_RUN_PARAMETER - Static variable in class net.sf.basedb.plugins.util.Parameters

The name of the parameter that is created by Parameters.logFileParameter(String, String, String)

dryRun - Variable in class net.sf.basedb.core.data.JobData

dryRun - Variable in class net.sf.basedb.core.PluginConfigurationRequest

dryRun - Variable in class net.sf.basedb.core.PluginResponse

dryRun - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

dryRun - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

dryRun - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

dryRunParameter(String, String, Boolean) - Static method in class net.sf.basedb.plugins.util.Parameters

Parameter definition that enable/disable dry-run of a plug-in.

dtdFile - Static variable in class net.sf.basedb.core.ExtendedProperties

The DTD which is used to validate the XML file.

dtdFile - Static variable in class net.sf.basedb.core.PredefinedQuery

The DTD which is used to validate the XML file.

dtdFile - Static variable in class net.sf.basedb.core.Presets

The DTD which is used to validate the XML data.

dtdFile - Static variable in class net.sf.basedb.core.RawDataTypes

The DTD which is used to validate the XML file.

dtdFile - Static variable in class net.sf.basedb.plugins.Base1PluginExecuter

dtdFile - Static variable in class net.sf.basedb.plugins.executor.ParameterDefinition

dtdFile - Variable in class net.sf.basedb.util.XmlUtil2.Validator

dtdFileName - Static variable in class net.sf.basedb.plugins.HelpImporter

dtdFileName - Static variable in class net.sf.basedb.plugins.PluginConfigurationImporter

DummyJobExecutor - Class in net.sf.basedb.clients.jobagent.executors

This is dummy job executor implementation which just sets the status of each job to Job.Status.DONE without actually executing the job.

DummyJobExecutor() - Constructor for class net.sf.basedb.clients.jobagent.executors.DummyJobExecutor

DummyService - Class in net.sf.basedb.clients.web.extensions.service

A dummy service implementation that prints out the current time on System.out every x seconds (default = 10) when the service is running.

DummyService() - Constructor for class net.sf.basedb.clients.web.extensions.service.DummyService

duplicateFeatureErrorParameter - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

duplicateFeatureErrorParameter - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

DuplicateWizardException - Exception in net.sf.basedb.clients.web

This exception is thrown when a plug-in configuration wizard is open and the user tries to open a second one.

DuplicateWizardException() - Constructor for exception net.sf.basedb.clients.web.DuplicateWizardException

Create a new exception.

DuplicateWizardException(String) - Constructor for exception net.sf.basedb.clients.web.DuplicateWizardException

Create a new exception with a message.

DuplicateWizardException(String, Throwable) - Constructor for exception net.sf.basedb.clients.web.DuplicateWizardException

Create a new exception with a cause and a message.

DuplicateWizardException(Throwable) - Constructor for exception net.sf.basedb.clients.web.DuplicateWizardException

Create a new exception with a cause.

Dynamic - Class in net.sf.basedb.core.query

A factory class to create expressions, joins, etc. that are only used by queries in the dynamic database.

Dynamic() - Constructor for class net.sf.basedb.core.query.Dynamic

DynamicActionAttribute - Class in net.sf.basedb.clients.web.extensions

Class for holding the name and value of a dynamic action attribute.

DynamicActionAttribute(String, String) - Constructor for class net.sf.basedb.clients.web.extensions.DynamicActionAttribute

Create a new dynamic action attribute.

DynamicActionAttributes - Interface in net.sf.basedb.clients.web.extensions

Supplementary interface for actions that need to be able to support dynamic attributes that are not pre-defined by the actual Action.

DynamicActionAttributeSupport - Class in net.sf.basedb.clients.web.extensions

Abstract base class intended to be extended by Action implementations that want to support dynamic action attributes.

DynamicActionAttributeSupport() - Constructor for class net.sf.basedb.clients.web.extensions.DynamicActionAttributeSupport

dynamicAttributes - Variable in class net.sf.basedb.clients.web.extensions.AbstractJspFactory

dynamicAttributes - Variable in class net.sf.basedb.clients.web.extensions.DynamicActionAttributeSupport

dynamicAttributes - Variable in class net.sf.basedb.clients.web.taglib.StylableTag

dynamicAttributes - Variable in class net.sf.basedb.clients.web.taglib.tab.Tab

dynamicCatalog - Static variable in class net.sf.basedb.core.Application

The name of the dynamic database.

dynamicDbIndexes(boolean, boolean, boolean) - Static method in class net.sf.basedb.core.HibernateUtil

Prints a lot of useful stuff about the dynamic database to standard output.

DynamicExtraValueQuery - Class in net.sf.basedb.core

Represents a query for extra values in the dynamic database.

DynamicExtraValueQuery(DataCube, VirtualTable, VirtualColumn...) - Constructor for class net.sf.basedb.core.DynamicExtraValueQuery

Create a new dynamic query.

DynamicField - Interface in net.sf.basedb.util.export.spotdata

Represents a spot or reporter field that is going to be exported from a bioassay set.

DynamicFilter - Interface in net.sf.basedb.util

This interface is used together with the BioAssaySetFilterUtil class to help a plugin filter the data of a bioassay set.

DynamicJoin - Class in net.sf.basedb.core

Represents a join between two virtual tables in a dynamic query: leftTable JOIN rightTable ON columns.

DynamicJoin(VirtualDb, JoinType, VirtualTable, VirtualColumn...) - Constructor for class net.sf.basedb.core.DynamicJoin

Create a new join using the root entity table as the left table.

DynamicJoin(VirtualDb, JoinType, VirtualTable, VirtualColumn[], VirtualTable, VirtualColumn[]) - Constructor for class net.sf.basedb.core.DynamicJoin

Create a new join between two tables with possible different colum names in the left and right tables.

DynamicJoin(VirtualDb, JoinType, VirtualTable, VirtualTable, VirtualColumn...) - Constructor for class net.sf.basedb.core.DynamicJoin

Create a new join between two tables.

DynamicPositionQuery - Class in net.sf.basedb.core

Represents a query for position information against the dynamic database.

DynamicPositionQuery(BioAssaySet) - Constructor for class net.sf.basedb.core.DynamicPositionQuery

Create a new dynamic query.

DynamicPositionQuery(Experiment) - Constructor for class net.sf.basedb.core.DynamicPositionQuery

DynamicPositionQueryJoiners - Class in net.sf.basedb.core

This class collects AutoJoiner:s for DynamicPositionQuery queries.

DynamicPositionQueryJoiners() - Constructor for class net.sf.basedb.core.DynamicPositionQueryJoiners

DynamicPositionQueryJoiners.ExtraValueJoiner - Class in net.sf.basedb.core

Joiner for extra values.

DynamicPositionQueryJoiners.ReporterJoiner - Class in net.sf.basedb.core

Joiner for reporters

DynamicPositionQueryJoiners.ReporterListJoiner - Class in net.sf.basedb.core

Auto joiner for reporter lists.

DynamicQuery - Class in net.sf.basedb.core

Represents a query against the dynamic database.

DynamicQuery(DataCube, VirtualTable, IntensityTransform) - Constructor for class net.sf.basedb.core.DynamicQuery

Create a new dynamic query.

DynamicQuery(VirtualDb, VirtualTable) - Constructor for class net.sf.basedb.core.DynamicQuery

Create a new non-restricted dynamic query.

DynamicQueryWrapper - Class in net.sf.basedb.clients.web.plugins

A query wrapper for DynamicQuery:s.

DynamicQueryWrapper(SqlQuery) - Constructor for class net.sf.basedb.clients.web.plugins.DynamicQueryWrapper

Create a new query wrapper.

DynamicRawDataQuery - Class in net.sf.basedb.core

Represents a query for raw data in a "dynamic" way.

DynamicRawDataQuery(RawBioAssay) - Constructor for class net.sf.basedb.core.DynamicRawDataQuery

Create a new dynamic query for raw data.

DynamicRawDataQuery(RawDataType) - Constructor for class net.sf.basedb.core.DynamicRawDataQuery

Create a new dynamic query for raw data.

DynamicRawDataQuery.RawBioAssayJoiner - Class in net.sf.basedb.core

Auto joiner for raw bioassays.

DynamicRawDataQuery.ReporterJoiner - Class in net.sf.basedb.core

Auto joiner for reporters.

DynamicRawDataQuery.ReporterListJoiner - Class in net.sf.basedb.core

Auto joiner for reporter lists.

DynamicReporterQuery - Class in net.sf.basedb.core

Represents a query for reporter data in a "dynamic" way.

DynamicReporterQuery() - Constructor for class net.sf.basedb.core.DynamicReporterQuery

Create a new dynamic query for reporter data.

DynamicReporterQuery(VirtualDb) - Constructor for class net.sf.basedb.core.DynamicReporterQuery

Create a new dynamic query for reporter data using cloned reporter information.

DynamicReporterQuery.MasterReporterJoiner - Class in net.sf.basedb.core

Auto joiner for master reporter table.

DynamicReporterQuery.ReporterListJoiner - Class in net.sf.basedb.core

Auto joiner for reporter lists.

DynamicRestriction - Class in net.sf.basedb.core

Creates a restriction that compares a dynamic column with a constant value: tableAlias.column = value or queryRootAlias.column = value

DynamicRestriction(VirtualColumn, int) - Constructor for class net.sf.basedb.core.DynamicRestriction

Create a new restriction for column in the root entity of the query: queryRootAlias.column = value.

DynamicRestriction(VirtualTable, VirtualColumn, int) - Constructor for class net.sf.basedb.core.DynamicRestriction

Create a new restriction for column in a joined table: tableAlias.column = value.

DynamicResultIterator - Class in net.sf.basedb.core

An iterator view of the result of an AbstractSqlQuery.

DynamicResultIterator(ResultSet, long, int) - Constructor for class net.sf.basedb.core.DynamicResultIterator

Create a new result iterator.

DynamicResultIterator.SqlResultImpl - Class in net.sf.basedb.core

Implements the SqlResult interface.

dynamicSchema - Static variable in class net.sf.basedb.core.Application

The name of the dynamic schema.

DynamicSpotQuery - Class in net.sf.basedb.core

Represents a query for spot information in the dynamic database.

DynamicSpotQuery(BioAssaySet) - Constructor for class net.sf.basedb.core.DynamicSpotQuery

Create a new dynamic query.

DynamicSpotQueryJoiners - Class in net.sf.basedb.core

This class collects AutoJoiner:s for DynamicSpotQuery queries.

DynamicSpotQueryJoiners() - Constructor for class net.sf.basedb.core.DynamicSpotQueryJoiners

DynamicSpotQueryJoiners.ExtraValueJoiner - Class in net.sf.basedb.core

Joiner for extra values.

DynamicSpotQueryJoiners.RawDataJoiner - Class in net.sf.basedb.core

Joiner for raw data.

DynamicSpotQueryJoiners.ReporterJoiner - Class in net.sf.basedb.core

Joiner for reporters

DynamicSpotQueryJoiners.ReporterListJoiner - Class in net.sf.basedb.core

Joiner for reporter lists.

DynamicUtil - Class in net.sf.basedb.clients.web

This class is used to collect some useful methods for building and executing dynamic queries.

DynamicUtil() - Constructor for class net.sf.basedb.clients.web.DynamicUtil

DynamicUtil.SelectedInfo - Class in net.sf.basedb.clients.web

E

e - Variable in class net.sf.basedb.core.query.BetweenRestriction

e - Variable in class net.sf.basedb.core.query.CountExpression

e - Variable in class net.sf.basedb.core.query.GeometricMeanExpression

e - Variable in class net.sf.basedb.core.query.MaxExpression

e - Variable in class net.sf.basedb.core.query.MeanExpression

e - Variable in class net.sf.basedb.core.query.MinExpression

e - Variable in class net.sf.basedb.core.query.QuadraticMeanExpression

e - Variable in class net.sf.basedb.core.query.RlikeRestriction

e - Variable in class net.sf.basedb.core.query.SumExpression

e1 - Variable in class net.sf.basedb.core.query.AbsExpression

e1 - Variable in class net.sf.basedb.core.query.AddExpression

e1 - Variable in class net.sf.basedb.core.query.DivideExpression

e1 - Variable in class net.sf.basedb.core.query.EqRestriction

e1 - Variable in class net.sf.basedb.core.query.ExpExpression

e1 - Variable in class net.sf.basedb.core.query.ExpressionSelect

e1 - Variable in class net.sf.basedb.core.query.GteqRestriction

e1 - Variable in class net.sf.basedb.core.query.GtRestriction

e1 - Variable in class net.sf.basedb.core.query.InRestriction

e1 - Variable in class net.sf.basedb.core.query.LikeRestriction

e1 - Variable in class net.sf.basedb.core.query.LogExpression

e1 - Variable in class net.sf.basedb.core.query.LteqRestriction

e1 - Variable in class net.sf.basedb.core.query.LtRestriction

e1 - Variable in class net.sf.basedb.core.query.MultiplyExpression

e1 - Variable in class net.sf.basedb.core.query.NegateExpression

e1 - Variable in class net.sf.basedb.core.query.NeqRestriction

e1 - Variable in class net.sf.basedb.core.query.SqrtExpression

e1 - Variable in class net.sf.basedb.core.query.SubtractExpression

e1 - Variable in class net.sf.basedb.core.query.ToDateExpression

e2 - Variable in class net.sf.basedb.core.query.AddExpression

e2 - Variable in class net.sf.basedb.core.query.DivideExpression

e2 - Variable in class net.sf.basedb.core.query.EqRestriction

e2 - Variable in class net.sf.basedb.core.query.GteqRestriction

e2 - Variable in class net.sf.basedb.core.query.GtRestriction

e2 - Variable in class net.sf.basedb.core.query.InRestriction

e2 - Variable in class net.sf.basedb.core.query.LikeRestriction

e2 - Variable in class net.sf.basedb.core.query.LteqRestriction

e2 - Variable in class net.sf.basedb.core.query.LtRestriction

e2 - Variable in class net.sf.basedb.core.query.MultiplyExpression

e2 - Variable in class net.sf.basedb.core.query.NeqRestriction

e2 - Variable in class net.sf.basedb.core.query.SubtractExpression

EDIT_ITEMS - Static variable in class net.sf.basedb.clients.web.extensions.edit.EditUtil

An array containing all items that we are registering extension points for.

EditUtil - Class in net.sf.basedb.clients.web.extensions.edit

Utility class for handling edit-dialog related extensions.

EditUtil() - Constructor for class net.sf.basedb.clients.web.extensions.edit.EditUtil

ekskey(byte[], byte[]) - Method in class net.sf.basedb.util.bcrypt.BCrypt

Perform the "enhanced key schedule" step described by Provos and Mazieres in "A Future-Adaptable Password Scheme" http://www.openbsd.org/papers/bcrypt-paper.ps

ElementIterator(Iterator<Tree.Entry<E>>) - Constructor for class net.sf.basedb.util.Tree.ElementIterator

elements(String, String) - Static method in class net.sf.basedb.core.query.Hql

Create an elements expression for a property that is a collection of values.

elseExpression - Variable in class net.sf.basedb.core.query.CaseExpression

email - Variable in class net.sf.basedb.core.authentication.ExtraUserInformation

email - Variable in class net.sf.basedb.core.data.PluginDefinitionData

email - Variable in class net.sf.basedb.core.data.UserData

email - Variable in class net.sf.basedb.core.plugin.AboutImpl

email - Variable in class net.sf.basedb.util.extensions.AboutBean

email - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredAbout

EMAIL_REGEXP - Static variable in class net.sf.basedb.clients.web.util.HTML

This pattern can be used to find email addresses.

EMAIL_REGEXP - Static variable in class net.sf.basedb.util.EmailUtil

This pattern can be used to find email addresses.

EmailUtil - Class in net.sf.basedb.util

Utility class for email sending.

EmailUtil() - Constructor for class net.sf.basedb.util.EmailUtil

EMPTY_CELL - Static variable in class net.sf.basedb.util.excel.ExcelValue

EMPTY_STRING - Static variable in class net.sf.basedb.clients.web.fileupload.FileUpload

emptyCell() - Static method in class net.sf.basedb.util.excel.ExcelValue

This creates a blank cell.

emptyIsNull - Variable in class net.sf.basedb.util.parser.FlatFileParser.Data

emptyIsNull - Variable in class net.sf.basedb.util.parser.FlatFileParser

If null should be returned for empty columns (instead of an empty string).

emptyMap - Variable in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring

emptyMap - Variable in class net.sf.basedb.core.Job.SignalKeyring

emptyMap - Variable in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring

emptySet - Variable in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring

emptySet - Variable in class net.sf.basedb.core.Job.SignalKeyring

emptySet - Variable in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring

EMTPY_OBJECT_ARRAY - Static variable in class net.sf.basedb.core.log.LoggingInterceptor

EMTPY_STRING_ARRAY - Static variable in class net.sf.basedb.core.log.LoggingInterceptor

EMTPY_TYPE_ARRAY - Static variable in class net.sf.basedb.core.log.LoggingInterceptor

enableAllInFile(String, boolean) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Enable or disable all extensions and extension points in a file.

enableAnnotationTypes(Connection, List<Integer>) - Method in class net.sf.basedb.core.MigrateRbaToDba

Make sure that the annotation types that are used by the migrated raw bioassays are enabled for derived bioassays.

enabled - Variable in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

enabled - Variable in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean

enabled - Variable in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean

enabled - Variable in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory

enabled - Static variable in class net.sf.basedb.clients.web.servlet.RssNewsFeed

enabled - Variable in class net.sf.basedb.clients.web.taglib.Icon

If the icon should be enabled or not (if an onclick has been set).

enabled - Variable in class net.sf.basedb.clients.web.taglib.menu.Menuitem

If the menu item is enabled.

enabled - Variable in class net.sf.basedb.clients.web.taglib.menu.Submenu

If the menu item is enabled.

enabled - Variable in class net.sf.basedb.clients.web.taglib.path.PathElement

enabled - Static variable in class net.sf.basedb.util.EmailUtil

enabledClazz - Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

enabledClazz - Variable in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

enableDeviceVerification(String) - Method in class net.sf.basedb.core.User

Verify the email and enables device verification.

enabledFilters - Variable in class net.sf.basedb.core.QueryRuntimeFilterManager

The names of already enabled filters.

enabledIcon - Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

enabledIcon - Variable in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

enableDownloadLink - Variable in class net.sf.basedb.clients.web.taglib.PropertyValue

Use for files only, if the view/download link should be enabled or not.

enabledPermission - Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

enabledPermission - Variable in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

enabledStyle - Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

enabledStyle - Variable in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

enabledTitle - Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

enabledTitle - Variable in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

enabledTooltip - Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

enabledTooltip - Variable in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

enableEditLink - Variable in class net.sf.basedb.clients.web.formatter.AutoLinkFormatter

enableEditLink - Variable in class net.sf.basedb.clients.web.formatter.LinkedFileFormatter

enableEditLink - Variable in class net.sf.basedb.clients.web.formatter.LinkedItemFormatter

enableEditLink - Variable in class net.sf.basedb.clients.web.taglib.PropertyValue

Possible to open an edit popup or not with the linked property

enableExtension(String, boolean) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Enable/disable an extension.

enableExtension(String, boolean) - Method in class net.sf.basedb.util.extensions.manager.Settings

Enable/disable an extension.

enableExtensionPoint(String, boolean) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Enable/disable an extension point.

enableExtensionPoint(String, boolean) - Method in class net.sf.basedb.util.extensions.manager.Settings

Enable/disable an extension point.

enableFetchProfile(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

enableFileTypes(Connection, List<Integer>) - Method in class net.sf.basedb.core.MigrateRbaToDba

Make sure that the data file types that are used by the migrated raw bioassays are enabled for derived bioassays.

enableFilter(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

enableFilter(String) - Method in class net.sf.basedb.core.QueryRuntimeFilterManager

Enable a filter, unless it has already been enabled

enableFilter(Session, String) - Static method in class net.sf.basedb.core.HibernateUtil

Enable the filter with the given name.

enableFilters(DbControl) - Method in class net.sf.basedb.core.AbstractEntityQuery

Enable runtime query filters for the query.

enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.Annotation.QueryRuntimeFilterImpl

enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.AnnotationSet.QueryRuntimeFilterImpl

enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.FileSet.QueryRuntimeFilterImpl

enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.FileSetMember.QueryRuntimeFilterImpl

enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.Group.QueryRuntimeFilterImpl

enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.Message.QueryRuntimeFilterImpl

enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.News.QueryRuntimeFilterImpl

enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.Project.QueryRuntimeFilterImpl

enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in interface net.sf.basedb.core.QueryRuntimeFilter

Enable the filters based on the options specified by the query and the logged in users permissions.

enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.QueryRuntimeFilterFactory.AnnotatableFilter

enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.QueryRuntimeFilterFactory.BasicFilter

enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.QueryRuntimeFilterFactory.ChainedFilter

Call QueryRuntimeFilter.enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) for each of the chained filters.

enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.QueryRuntimeFilterFactory.ChildFilter

enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.QueryRuntimeFilterFactory.DenyAllFilter

enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.QueryRuntimeFilterFactory.OwnableFilter

enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.QueryRuntimeFilterFactory.RemovableFilter

enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.QueryRuntimeFilterFactory.ShareableFilter

enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.Quota.QueryRuntimeFilterImpl

enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.Role.QueryRuntimeFilterImpl

enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.Session.QueryRuntimeFilterImpl

enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.User.QueryRuntimeFilterImpl

enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.UserDevice.QueryRuntimeFilterImpl

enableForItem(Item) - Method in class net.sf.basedb.core.AnnotationType

Enable this annotation type to be used for items of the specified type.

enablePropertyLink - Variable in class net.sf.basedb.clients.web.taglib.PropertyValue

A link to the property item or not.

enableViewDownload - Variable in class net.sf.basedb.clients.web.formatter.AutoLinkFormatter

enableViewDownload - Variable in class net.sf.basedb.clients.web.formatter.LinkedFileFormatter

encipher(int[], int) - Method in class net.sf.basedb.util.bcrypt.BCrypt

Blowfish encipher a single 64-bit block encoded as two 32-bit halves

encode(String) - Method in interface net.sf.basedb.util.encode.EncoderDecoder

encode(String) - Method in class net.sf.basedb.util.encode.IdentityEncoderDecoder

encode(String) - Method in class net.sf.basedb.util.encode.TabCrLfEncoderDecoder

encode(String) - Method in class net.sf.basedb.util.encode.ToSpaceEncoderDecoder

encode_base64(byte[], int) - Static method in class net.sf.basedb.util.bcrypt.BCrypt

Encode a byte array using bcrypt's slightly-modified base64 encoding scheme.

encodeAll(Collection<String>, EncoderDecoder) - Static method in class net.sf.basedb.util.encode.EncodeUtil

Encode all strings in a collection.

encodeAndJoin(Collection<String>, EncoderDecoder, String, boolean) - Static method in class net.sf.basedb.util.encode.EncodeUtil

Encode all strings in a collection and join them into a single string.

encoder - Variable in class net.sf.basedb.util.bfs.MetadataWriter

encoder - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil

encoder - Variable in class net.sf.basedb.util.export.TableWriter

EncoderDecoder - Interface in net.sf.basedb.util.encode

Interface for encoding and decoding strings to make them work in a certain context.

encodeTags(String) - Static method in class net.sf.basedb.clients.web.util.HTML

Scans a string for HTML tags and replaces all & with &amp;, < with &lt;, > with &gt; and all " with "

encodeTags(String, String) - Static method in class net.sf.basedb.clients.web.util.HTML

Scans a string for HTML tags and replaces all < and > for tags not found in the safeTags pattern with &lt; and &gt; respectively.

encodeTags(String, Pattern) - Static method in class net.sf.basedb.clients.web.util.HTML

Scans a string for HTML tags and replaces all < and > for tags not found matching the safeTags pattern with &lt; and &gt; respectively.

EncodeUtil - Class in net.sf.basedb.util.encode

Utility functions for encoding/decoding strings.

EncodeUtil() - Constructor for class net.sf.basedb.util.encode.EncodeUtil

encodeValue(String) - Method in class net.sf.basedb.util.bfs.MetadataWriter

Encode a value for use in a BFS file.

encryptPassword(String) - Static method in class net.sf.basedb.core.User

Encrypt the plain-text password.

end - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream

end - Variable in class net.sf.basedb.util.ChainedProgressReporter

end(boolean) - Method in class net.sf.basedb.clients.web.plugins.SimpleExport

end(boolean) - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin

Called just after everything has been committed to the database, or immediately after an error has ocurred.

end(boolean) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

Called just after the last line of the file has been parsed, or immediately after an error has ocurred.

end(boolean) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter

Now it's time to update the items in the cache with the new annotation values.

end(boolean) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin

end(boolean) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

end(boolean) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

end(boolean) - Method in class net.sf.basedb.plugins.BfsExporterPlugin

end(boolean) - Method in class net.sf.basedb.plugins.GalExporter

end(boolean) - Method in class net.sf.basedb.plugins.HelpExporter

end(boolean) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter

If successful: Close batchers Associate with experiment if there is one Commit If not successful: Delete raw bioassays that has been created Rollback

end(boolean) - Method in class net.sf.basedb.plugins.PackedFileExporter

end(boolean) - Method in class net.sf.basedb.plugins.PlateFlatFileImporter

Close and commit/rollback and DbControl.

end(boolean) - Method in class net.sf.basedb.plugins.PlateMappingExporter

end(boolean) - Method in class net.sf.basedb.plugins.PlateMappingImporter

Close and commit/rollback the DbControl.

end(boolean) - Method in class net.sf.basedb.plugins.PluginConfigurationExporter

end(boolean) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter

end(boolean) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter

Close and commit/rollback the RawDataBatcher and DbControl.

end(boolean) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter

Close and commit/rollback the ReporterBatcher and DbControl.

end(boolean) - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

Close and commit/rollback the FeatureBatcher and DbControl.

END_OF_FILE_EVENT - Static variable in class net.sf.basedb.util.bfs.AnnotationParser

Event type that is issued when the end-of-file had been reached.

END_OF_FILE_EVENT - Static variable in class net.sf.basedb.util.bfs.DataParser

Event type that is issued when the end-of-file had been reached.

END_OF_FILE_EVENT - Static variable in class net.sf.basedb.util.bfs.MetadataParser

Event type that is issued when the end-of-file had been reached.

endColumnDefinitions() - Method in class net.sf.basedb.clients.web.taglib.table.Table

endColumnFilters() - Method in class net.sf.basedb.clients.web.taglib.table.Table

endDate - Variable in class net.sf.basedb.core.data.NewsData

endDocument(ProgressReporter) - Method in interface net.sf.basedb.clients.web.plugins.ExportTemplate

End writing the document.

endDocument(ProgressReporter) - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate

Do nothing.

endDocument(ProgressReporter) - Method in class net.sf.basedb.clients.web.plugins.XlsxTemplate

Write the Excel workbook to the output stream and close.

endDocument(ProgressReporter) - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate

Close the document tags.

ended - Variable in class net.sf.basedb.core.data.JobData

endExport(RuntimeException) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

End the export and clean up/close all aquired resources.

endExport(RuntimeException) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter

endExport(RuntimeException) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter

Clean up.

endExport(RuntimeException) - Method in class net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter

endExport(RuntimeException) - Method in class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter

endIndex - Variable in class net.sf.basedb.core.FastAnnotationLoader.FastIterator

endItem() - Method in interface net.sf.basedb.clients.web.plugins.ExportTemplate

End writing an item

endItem() - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate

Write a newline.

endItem() - Method in class net.sf.basedb.clients.web.plugins.XlsxTemplate

Do nothing.

endItem() - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate

Write the current item element to the export stream.

endTime - Variable in class net.sf.basedb.util.extensions.manager.ProcessResults

endX - Variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin

ENERGY - Static variable in class net.sf.basedb.core.Quantity

The id for the Quantity object representing energy.

EngineFactory - Class in net.sf.basedb.core.dbengine

Creates DbEngine objects based on the Hibernate dialect.

EngineFactory() - Constructor for class net.sf.basedb.core.dbengine.EngineFactory

EnhancedThreadSignalHandler - Class in net.sf.basedb.core.signal

An extension to the thread signal handler that supports any number of signals.

EnhancedThreadSignalHandler(Collection<Signal>) - Constructor for class net.sf.basedb.core.signal.EnhancedThreadSignalHandler

Create a new signal handler that supports the specified signals.

EnhancedThreadSignalHandler(Signal...) - Constructor for class net.sf.basedb.core.signal.EnhancedThreadSignalHandler

Create a signal handler that supports the specified signals.

ensureProductParentCorrectness(BioMaterialEventData) - Static method in class net.sf.basedb.core.BioMaterialEvent

Ensure that the MeasuredBioMaterial.getParent() and MeasuredBioMaterial.getParentType() reflect the current sources collection.

entity - Variable in class net.sf.basedb.core.log.EntityDetails

entity(BasicItem) - Static method in class net.sf.basedb.core.query.Hql

Create an expression representing an item which is a subclass of BasicItem.

entity(BasicData) - Static method in class net.sf.basedb.core.query.Hql

Create an expression representing an item which is a subclass of BasicData, for example a reporter.

ENTITY_COLLECTION - Variable in class net.sf.basedb.core.PropertyFilter

EntityDetails - Class in net.sf.basedb.core.log

Contains detailed information about the changes made to an entity during a transaction.

EntityDetails(Object, ChangeType, Object[], Object[], String[], Type[]) - Constructor for class net.sf.basedb.core.log.EntityDetails

EntityLogger - Interface in net.sf.basedb.core.log

Entity logger implementations are created by a LogManagerFactory when a change to a logged entity has been detected.

EntityLogOptions - Class in net.sf.basedb.core.log

This class collect some static information related to logging for entities.

EntityLogOptions(Class<?>) - Constructor for class net.sf.basedb.core.log.EntityLogOptions

entityName - Variable in class net.sf.basedb.core.BasicBatcher

The entity name as known to Hibernate.

entityName - Variable in class net.sf.basedb.core.Metadata

entityParameter(String, Item) - Static method in class net.sf.basedb.core.query.Hql

Create an expression for a parameter which must be an entity of a specified type.

EntityPropertyPath(ClassMetadata, String, Type) - Constructor for class net.sf.basedb.core.Metadata.EntityPropertyPath

EntityQuery - Interface in net.sf.basedb.core.query

This a HQL query that return enitities, ie. items.

EntityQueryWrapper<R> - Class in net.sf.basedb.core.hibernate

Wraps a hibernate query and adds checks so that unsaved items aren't added to the query as parameters.

EntityQueryWrapper(Query<R>) - Constructor for class net.sf.basedb.core.hibernate.EntityQueryWrapper

entries - Variable in class net.sf.basedb.util.bfs.MetadataModel.Section

entries - Variable in class net.sf.basedb.util.Enumeration

entries - Variable in class net.sf.basedb.util.Tree

Entry(K, V) - Constructor for class net.sf.basedb.util.Enumeration.Entry

Entry(Tree<E>, E, Tree.Entry<E>) - Constructor for class net.sf.basedb.util.Tree.Entry

ENTRY_DATE - Static variable in class net.sf.basedb.core.ClonableProperty

The property name of the "static" property ReporterData.getEntryDate()

ENTRY_EVENT - Static variable in class net.sf.basedb.util.bfs.MetadataParser

Event type that is issued for each entry in a section in the order they are present in the file.

entryDate - Variable in class net.sf.basedb.core.data.AnnotationTypeCategoryData

entryDate - Variable in class net.sf.basedb.core.data.AnnotationTypeData

entryDate - Variable in class net.sf.basedb.core.data.ArrayBatchData

entryDate - Variable in class net.sf.basedb.core.data.ArrayDesignData

entryDate - Variable in class net.sf.basedb.core.data.ArraySlideData

entryDate - Variable in class net.sf.basedb.core.data.BioMaterialEventData

entryDate - Variable in class net.sf.basedb.core.data.BioPlateData

entryDate - Variable in class net.sf.basedb.core.data.BioPlateEventData

entryDate - Variable in class net.sf.basedb.core.data.BioSourceData

entryDate - Variable in class net.sf.basedb.core.data.ClientData

entryDate - Variable in class net.sf.basedb.core.data.DerivedBioAssayData

entryDate - Variable in class net.sf.basedb.core.data.ExperimentData

entryDate - Variable in class net.sf.basedb.core.data.ExtraValueTypeData

entryDate - Variable in class net.sf.basedb.core.data.FormulaData

entryDate - Variable in class net.sf.basedb.core.data.GroupData

entryDate - Variable in class net.sf.basedb.core.data.HardwareData

entryDate - Variable in class net.sf.basedb.core.data.ItemSubtypeData

entryDate - Variable in class net.sf.basedb.core.data.KitData

entryDate - Variable in class net.sf.basedb.core.data.MimeTypeData

entryDate - Variable in class net.sf.basedb.core.data.NewsData

entryDate - Variable in class net.sf.basedb.core.data.PlateData

entryDate - Variable in class net.sf.basedb.core.data.PlateEventData

entryDate - Variable in class net.sf.basedb.core.data.PlateGeometryData

entryDate - Variable in class net.sf.basedb.core.data.PlateMappingData

entryDate - Variable in class net.sf.basedb.core.data.PlateTypeData

entryDate - Variable in class net.sf.basedb.core.data.PluginConfigurationData

entryDate - Variable in class net.sf.basedb.core.data.PluginDefinitionData

entryDate - Variable in class net.sf.basedb.core.data.PluginTypeData

entryDate - Variable in class net.sf.basedb.core.data.ProjectData

entryDate - Variable in class net.sf.basedb.core.data.ProtocolData

entryDate - Variable in class net.sf.basedb.core.data.QuotaTypeData

entryDate - Variable in class net.sf.basedb.core.data.RawBioAssayData

entryDate - Variable in class net.sf.basedb.core.data.ReporterCloneTemplateData

entryDate - Variable in class net.sf.basedb.core.data.ReporterData

entryDate - Variable in class net.sf.basedb.core.data.ReporterListData

entryDate - Variable in class net.sf.basedb.core.data.ReporterTypeData

entryDate - Variable in class net.sf.basedb.core.data.RoleData

entryDate - Variable in class net.sf.basedb.core.data.SoftwareData

entryDate - Variable in class net.sf.basedb.core.data.TagData

entryDate - Variable in class net.sf.basedb.core.data.UserData

entryDate - Variable in class net.sf.basedb.core.data.UserDeviceData

entryDate - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba

entryDate - Variable in class net.sf.basedb.core.ReporterBatcher

Date to to give new reporters.

entryIterator - Variable in class net.sf.basedb.util.Tree.ElementIterator

The entry iterator.

entryIterator() - Method in class net.sf.basedb.util.Tree

Create an iterator for the tree that returns entry object.

entryIterator(E) - Method in class net.sf.basedb.util.Tree

Create an iterator for the tree starting at a specific node.

EntryIterator(Tree.Entry<E>) - Constructor for class net.sf.basedb.util.Tree.EntryIterator

Create an iterator that starts at the specified entry.

enumClass - Variable in class net.sf.basedb.util.formatter.EnumFormatter

EnumConverter<T extends Enum<T>> - Class in net.sf.basedb.util.json

Converted implementation that create JSON objects with the NAME of enumeration.

EnumConverter() - Constructor for class net.sf.basedb.util.json.EnumConverter

enumeration - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

enumeration - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef

Options for enum.

enumeration - Variable in class net.sf.basedb.core.ParameterType

List of allowed values.

Enumeration<K,V> - Class in net.sf.basedb.util

Enumeration() - Constructor for class net.sf.basedb.util.Enumeration

ENUMERATION - Enum constant in enum class net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType

Enumeration.Entry<K,V> - Class in net.sf.basedb.util

enumerationColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

Column mapping parameter for "Enumeration".

enumerationMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

enumerationSplitter - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

enumerationSplitterRegexpParameter - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

Regular expression splitter parameter for enumerations.

enumerationValues - Variable in class net.sf.basedb.core.data.AnnotationTypeData

EnumFormatter<T extends Enum<T>> - Class in net.sf.basedb.util.formatter

Formatter implementation that converts an enum constant into it's name() as the formatted value.

EnumFormatter(Class<T>) - Constructor for class net.sf.basedb.util.formatter.EnumFormatter

Create a new formatter.

EnumFormatter(Class<T>, String) - Constructor for class net.sf.basedb.util.formatter.EnumFormatter

Create a new formatter.

enumOptions - Variable in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter

eof - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStatus

TRUE if the end of the stream is reached, FALSE otherwise

eof() - Method in class net.sf.basedb.clients.web.fileupload.FileUpload

Check if the end of the upload has been reached or not.

eof(int) - Method in class net.sf.basedb.util.charset.SimpleStringDetector

eof(int) - Method in interface net.sf.basedb.util.charset.StringDetector

This is called when the end of file has been reached and the checkLine method has returned false for all lines.

ep - Variable in class net.sf.basedb.clients.web.formatter.ExtendedPropertyFormatter

EP_ALL - Static variable in class net.sf.basedb.clients.web.extensions.list.ListColumnUtil

ID for the list column extension point that appear on all list pages.

EP_ALL - Static variable in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil

ID:s for the toolbar extension point that appear on all pages.

EP_ANNOTATABLE - Static variable in class net.sf.basedb.clients.web.extensions.list.ListColumnUtil

ID for the list column extension point that appear on all pages that list Annotatable items.

EP_ANNOTATABLE - Static variable in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil

ID:s for the toolbar extension point that appear on all pages that displays Annotatable items.

EP_OWNABLE - Static variable in class net.sf.basedb.clients.web.extensions.list.ListColumnUtil

ID for the list column extension point that appear on all pages that list Ownable items.

EP_OWNABLE - Static variable in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil

ID:s for the toolbar extension point that appear on all pages that displays Ownable items.

EP_PREFIX - Static variable in class net.sf.basedb.clients.web.extensions.list.ListColumnUtil

ID prefixes for list column extension point.

EP_PREFIX - Static variable in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil

ID prefixes for toolbar extension point.

EP_PREFIX_EDIT - Static variable in class net.sf.basedb.clients.web.extensions.edit.EditUtil

ID prefix for tabcontrol extension points on edit pages.

EP_PREFIX_SAVE - Static variable in class net.sf.basedb.clients.web.extensions.edit.EditUtil

ID prefix for tabcontrol extension points on edit pages.

EP_REMOVABLE - Static variable in class net.sf.basedb.clients.web.extensions.list.ListColumnUtil

ID for the list column extension point that appear on all pages that list Removable items.

EP_REMOVABLE - Static variable in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil

ID:s for the toolbar extension point that appear on all pages that displays Removable items.

EP_SHAREABLE - Static variable in class net.sf.basedb.clients.web.extensions.list.ListColumnUtil

ID for the list column extension point that appear on all pages that list Shareable items.

EP_SHAREABLE - Static variable in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil

ID:s for the toolbar extension point that appear on all pages that displays Shareable items.

eq(Expression, Expression) - Static method in class net.sf.basedb.core.query.Restrictions

Compare if two expressions are equal: new restriction = e1 == e2.

EQ - Enum constant in enum class net.sf.basedb.core.Operator

EqRestriction - Class in net.sf.basedb.core.query

Compare if two expressions are equal: e1 == e2, or e1 IS NULL

EqRestriction(Expression, Expression) - Constructor for class net.sf.basedb.core.query.EqRestriction

equals(Object) - Method in class net.sf.basedb.clients.web.extensions.ServletWrapperKey

equals(Object) - Method in class net.sf.basedb.clients.web.ModeInfo.ModeContext

equals(Object) - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey

equals(Object) - Method in class net.sf.basedb.core.AnnotationBetweenRestriction

This restriction is equal to another AnnotationBetweenRestriction if they have the same annotation type, upper and lower bound and inheritance setting.

equals(Object) - Method in class net.sf.basedb.core.AnnotationInRestriction

This restriction is equal to another AnnotationInRestriction if they have the same annotation type, list of values and inheritance setting.

equals(Object) - Method in class net.sf.basedb.core.AnnotationSimpleRestriction

This restriction is equal to another AnnotationSimpleRestriction if they have the same annotation type, operator, list of values and inheritance setting.

equals(Object) - Method in class net.sf.basedb.core.BasicItem

Check if this item is equal to another item.

equals(Object) - Method in class net.sf.basedb.core.BlockInfo

Check if this object is equal to another BlockInfo object.

equals(Object) - Method in class net.sf.basedb.core.ClonableProperty

equals(Object) - Method in class net.sf.basedb.core.ContextKey

Check if this object is equal to another ContextKey object.

equals(Object) - Method in class net.sf.basedb.core.data.BasicData

Check if this item is equal to another item.

equals(Object) - Method in class net.sf.basedb.core.data.BioMaterialData

It may happen that lazy-loaded proxies are put in the same collection as already loaded "real" objects in which case the BasicData.equals() method doesns't work.

equals(Object) - Method in class net.sf.basedb.core.data.ContextIndex

Check if this object is equal to another ContextIndex object.

equals(Object) - Method in class net.sf.basedb.core.data.FileTypeIndex

Check if this object is equal to another FileTypeIndex object.

equals(Object) - Method in class net.sf.basedb.core.data.GuiContextData

Check if this object is equal to another GuiContext object.

equals(Object) - Method in class net.sf.basedb.core.data.keyring.GroupGroups

Check if this object is equal to another GroupGroups object.

equals(Object) - Method in class net.sf.basedb.core.data.keyring.GroupKeys

Check if this object is equal to another GroupKeys object.

equals(Object) - Method in class net.sf.basedb.core.data.keyring.GroupProjects

Check if this object is equal to another GroupProjects object.

equals(Object) - Method in class net.sf.basedb.core.data.keyring.PluginKeys

Check if this object is equal to another RoleKeys object.

equals(Object) - Method in class net.sf.basedb.core.data.keyring.ProjectKeys

Check if this object is equal to another ProjectKeys object.

equals(Object) - Method in class net.sf.basedb.core.data.keyring.RoleKeys

Check if this object is equal to another RoleKeys object.

equals(Object) - Method in class net.sf.basedb.core.data.keyring.UserGroups

Check if this object is equal to another UserGroups object.

equals(Object) - Method in class net.sf.basedb.core.data.keyring.UserKeys

Check if this object is equal to another UserKeys object.

equals(Object) - Method in class net.sf.basedb.core.data.keyring.UserProjects

Check if this object is equal to another UserProjects object.

equals(Object) - Method in class net.sf.basedb.core.data.keyring.UserRoles

Check if this object is equal to another UserRoles object.

equals(Object) - Method in class net.sf.basedb.core.data.MappingCoordinate

Check if this object is equal to another MappingCoordinate object.

equals(Object) - Method in class net.sf.basedb.core.data.PlateCoordinate

Check if this object is equal to another PlateCoordinateData object.

equals(Object) - Method in class net.sf.basedb.core.data.QuotaIndex

Check if this object is equal to another QuotaIndex object.

equals(Object) - Method in class net.sf.basedb.core.data.ReporterListScoreData

equals(Object) - Method in class net.sf.basedb.core.data.VersionedParameter

Check if this object is equal to another VersionedParameter object.

equals(Object) - Method in class net.sf.basedb.core.DynamicJoin

This join is equal to another DynamicJoin if they join between the same tables using the same columns and join types.

equals(Object) - Method in class net.sf.basedb.core.DynamicRestriction

This restriction is equal to another DynamicRestriction if their table, column and values are equal.

equals(Object) - Method in class net.sf.basedb.core.ExtraValueExpression

This expression is equal to another ExtraValueExpression if they represents the same extra value.

equals(Object) - Method in class net.sf.basedb.core.ExtraValueJoin

This join is equal to another ExtraValueJoin if they join to the same extra value with the same join type.

equals(Object) - Method in class net.sf.basedb.core.FeatureCoordinate

Check if this object is equal to another FeatureCoordinate object.

equals(Object) - Method in class net.sf.basedb.core.HasAnnotationRestriction

This restriction is equal to another HasAnnotationRestriction if they have the same annotation type, inheritance setting and annotation check.

equals(Object) - Method in class net.sf.basedb.core.ItemProxy

Check if this item is equal to another item.

equals(Object) - Method in class net.sf.basedb.core.ItemResultList

equals(Object) - Method in class net.sf.basedb.core.MeanRawDataPropertyExpression

This expression is equal to another MeanRawDataPropertyExpression if they represent the same raw data property.

equals(Object) - Method in class net.sf.basedb.core.plugin.GuiContext

equals(Object) - Method in class net.sf.basedb.core.query.AbsExpression

This expression is equal to another AbsExpression if their child expressions are equal.

equals(Object) - Method in class net.sf.basedb.core.query.AddExpression

This expression is equal to another AddExpression if their child expressions are equal (ignoring the order).

equals(Object) - Method in class net.sf.basedb.core.query.AndRestriction

This restriction is equal to another AndRestriction if both contains the same restrictions (disregarding order).

equals(Object) - Method in class net.sf.basedb.core.query.AnnotationJoin

This join is equal to another AnnotationJoin if they join to the same annotation type with the same alias.

equals(Object) - Method in class net.sf.basedb.core.query.AnyToAnyRestriction

This expression is equal to another AnyToAnyRestriction if their named link, 'hasLink' and subquery restriction are the same.

equals(Object) - Method in class net.sf.basedb.core.query.AscOrder

This expression is equal to another AscOrder if their child expressions are equal.

equals(Object) - Method in class net.sf.basedb.core.query.BetweenRestriction

This restriction is equal to another BetweenRestriction if their child expressions are equal.

equals(Object) - Method in class net.sf.basedb.core.query.BooleanExpression

This expression is equal to another BooleanExpression if their values or restrictions are equal.

equals(Object) - Method in class net.sf.basedb.core.query.CaseExpression

This expression is equal to another CaseExpression if both contains the same when statements (disregarding order) and else expression.

equals(Object) - Method in class net.sf.basedb.core.query.ConditionalQueryElement

This query element is equal to another ConditionalQueryElement if their filter and child elements are equal.

equals(Object) - Method in class net.sf.basedb.core.query.CountExpression

This expression is equal to another CountExpression if their child expressions are equal and have the same DISTINCT setting.

equals(Object) - Method in class net.sf.basedb.core.query.DescOrder

This expression is equal to another DescOrder if their child expressions are equal.

equals(Object) - Method in class net.sf.basedb.core.query.DivideExpression

This expression is equal to another DivideExpression if their child expressions are equal.

equals(Object) - Method in class net.sf.basedb.core.query.EqRestriction

This restriction is equal to another EqRestriction if their child restrictions are equal (ignoring the order).

equals(Object) - Method in class net.sf.basedb.core.query.ExpExpression

This expression is equal to another ExpExpression if their child expressions are equal.

equals(Object) - Method in class net.sf.basedb.core.query.ExpressionSelect

This expression is equal to another ExpressionSelect if their child expressions and aliases are equal.

equals(Object) - Method in class net.sf.basedb.core.query.FloatExpression

This expression is equal to another FloatExpression if their values are equal.

equals(Object) - Method in class net.sf.basedb.core.query.GeometricMeanExpression

This expression is equal to another GeometricMeanExpression if their child expressions are equal.

equals(Object) - Method in class net.sf.basedb.core.query.GteqRestriction

This restriction is equal to another GteqRestriction if their child restrictions are equal.

equals(Object) - Method in class net.sf.basedb.core.query.GtRestriction

This restriction is equal to another GtRestriction if their child restrictions are equal.

equals(Object) - Method in class net.sf.basedb.core.query.HqlElementsExpression

This expression is equal to another HqlElementsExpression if their alias and property expressions are equal.

equals(Object) - Method in class net.sf.basedb.core.query.HqlEntityExpression

This expression is equal to another HqlEntityExpression if they represent the same item.

equals(Object) - Method in class net.sf.basedb.core.query.HqlEntityParameterExpression

This expression is equal to another HqlEntityParameterExpression if their names are equal.

equals(Object) - Method in class net.sf.basedb.core.query.HqlExpression

This expression is equal to another HqlExpression if their child expressions are equal.

equals(Object) - Method in class net.sf.basedb.core.query.HqlIndexExpression

This expression is equal to another HqlIndexExpression if their alias and property expressions are equal.

equals(Object) - Method in class net.sf.basedb.core.query.HqlInnerJoin

This join is equal to another HqlInnerJoin if they join to the same property with the same alias and use the same condition and fetch mode.

equals(Object) - Method in class net.sf.basedb.core.query.HqlLeftJoin

This join is equal to another HqlLeftJoin if they join to the same property with the same alias and use the same condition and fetch mode.

equals(Object) - Method in class net.sf.basedb.core.query.HqlPropertyExpression

This expression is equal to another HqlPropertyExpression if their alias, property and index expressions are equal.

equals(Object) - Method in class net.sf.basedb.core.query.HqlRightJoin

This join is equal to another HqlRightJoin if they join to the same property with the same alias and use the same condition.

equals(Object) - Method in class net.sf.basedb.core.query.HqlSizeExpression

This expression is equal to another HqlSizeExpression if their alias and property expressions are equal.

equals(Object) - Method in class net.sf.basedb.core.query.InRestriction

This expression is equal to another InRestriction if both contains the same main expressions and list of expressions (disregarding order).

equals(Object) - Method in class net.sf.basedb.core.query.IntegerExpression

This expression is equal to another IntegerExpression if their values are equal.

equals(Object) - Method in class net.sf.basedb.core.query.LikeRestriction

This restriction is equal to another LikeRestriction if their child restrictions are equal.

equals(Object) - Method in class net.sf.basedb.core.query.LogExpression

This expression is equal to another LogExpression if their child expressions and bases are equal.

equals(Object) - Method in class net.sf.basedb.core.query.LteqRestriction

This restriction is equal to another LteqRestriction if their child restrictions are equal.

equals(Object) - Method in class net.sf.basedb.core.query.LtRestriction

This restriction is equal to another LtRestriction if their child restrictions are equal.

equals(Object) - Method in class net.sf.basedb.core.query.MaxExpression

This expression is equal to another MaxExpression if their child expressions are equal.

equals(Object) - Method in class net.sf.basedb.core.query.MeanExpression

This expression is equal to another MeanExpression if their child expressions are equal.

equals(Object) - Method in class net.sf.basedb.core.query.MinExpression

This expression is equal to another MinExpression if their child expressions are equal.

equals(Object) - Method in class net.sf.basedb.core.query.MultiplyExpression

This expression is equal to another MultiplyExpression if their child expressions are equal (ignoring the order).

equals(Object) - Method in class net.sf.basedb.core.query.NegateExpression

This expression is equal to another NegateExpression if their child expressions are equal.

equals(Object) - Method in class net.sf.basedb.core.query.NeqRestriction

This restriction is equal to another NeqRestriction if their child restrictions are equal (ignoring the order).

equals(Object) - Method in class net.sf.basedb.core.query.NotRestriction

This restriction is equal to another NotRestriction if their child restrictions are equal.

equals(Object) - Method in class net.sf.basedb.core.query.OrRestriction

This restriction is equal to another OrRestriction if both contains the same restrictions (disregarding order).

equals(Object) - Method in class net.sf.basedb.core.query.ParameterExpression

This expression is equal to another ParameterExpression if their names expressions are equal.

equals(Object) - Method in class net.sf.basedb.core.query.PowerExpression

This expression is equal to another MultiplyExpression if their child expressions are equal.

equals(Object) - Method in class net.sf.basedb.core.query.QuadraticMeanExpression

This expression is equal to another QuadraticMeanExpression if their child expressions are equal.

equals(Object) - Method in class net.sf.basedb.core.query.QueryParameter

equals(Object) - Method in class net.sf.basedb.core.query.ReporterListExpression

This expression is equal to another ReporterListExpression if they use the same property from the same reporter list and uses the same auto join type.

equals(Object) - Method in class net.sf.basedb.core.query.RlikeRestriction

This restriction is equal to another RlikeRestriction if their child restrictions are equal.

equals(Object) - Method in class net.sf.basedb.core.query.SelectedExpression

This expression is equal to another SelectedExpression if their child expressions are equal.

equals(Object) - Method in class net.sf.basedb.core.query.SharedToRestriction

This restriction is equal to another SharedToRestriction if their child restrictions and other parameters are equal.

equals(Object) - Method in class net.sf.basedb.core.query.SqlColumnExpression

This expression is equal to another SqlColumnExpression if their aliases and columns are equal.

equals(Object) - Method in class net.sf.basedb.core.query.SqrtExpression

This expression is equal to another SqrtExpression if their child expressions are equal.

equals(Object) - Method in class net.sf.basedb.core.query.SubqueryExpression

This expression is equal to another SubqueryExpression if they use the same operator and reference the same subquery instance.

equals(Object) - Method in class net.sf.basedb.core.query.SubtractExpression

This expression is equal to another AddExpression if their child expressions are equal.

equals(Object) - Method in class net.sf.basedb.core.query.SumExpression

This expression is equal to another SumExpression if their child expressions are equal.

equals(Object) - Method in class net.sf.basedb.core.query.ToDateExpression

This expression is equal to another ToDateExpression if their child expressions are equal.

equals(Object) - Method in class net.sf.basedb.core.query.VirtualColumnExpression

This expression is equal to another VirtualColumnExpression if their tables and columns are equal.

equals(Object) - Method in class net.sf.basedb.core.query.WhenStatement

This statement is equal to another WhenStatement if both have equal conditions and values.

equals(Object) - Method in class net.sf.basedb.core.RawBioAssayPropertyExpression

This expression is equal to another RawBioAssayPropertyExpression if they represent the same reporter property.

equals(Object) - Method in class net.sf.basedb.core.RawDataPropertyExpression

This expression is equal to another RawDataPropertyExpression if they represent the same raw data property.

equals(Object) - Method in class net.sf.basedb.core.RawDataType

equals(Object) - Method in class net.sf.basedb.core.RealJoin

This join is equal to another RealJoin if they join between the same tables using the same columns and join types.

equals(Object) - Method in class net.sf.basedb.core.ReporterListJoin

This join is equal to another ReporterListJoin if they join to the same reporter list with the same join type.

equals(Object) - Method in class net.sf.basedb.core.ReporterPropertyExpression

This expression is equal to another ReporterPropertyExpression if they represent the same reporter property.

equals(Object) - Method in class net.sf.basedb.core.SessionControl.MainContext

equals(Object) - Method in class net.sf.basedb.core.signal.Signal

Two signals are equal if they have the same ID.

equals(Object) - Method in class net.sf.basedb.core.VirtualColumn

A virtual column is equal to another if both have the same name.

equals(Object) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField

An extended dynamic field is equal to another field if their parent fields equal.

equals(Object) - Method in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper

A wrapper is equal to another if they references the same item and chain of extracts.

equals(Object) - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics

equals(Object) - Method in class net.sf.basedb.util.export.spotdata.AnnotationAssayField

An assay field is equal to another assay field if it uses the same annotation type and has the same title.

equals(Object) - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField

An assay field is equal to another assay field if it uses the same property and has the same title.

equals(Object) - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField

A jep dynamic field is equal to another field if it uses the same jep expression and has the same title.

equals(Object) - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField

A dynamic field is equal to another field if it uses the same expression and has the same title.

equals(Object) - Method in class net.sf.basedb.util.extensions.manager.ExtensionKey

equals(Object) - Method in class net.sf.basedb.util.extensions.manager.ExtensionPointKey

equals(Object) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile

equals(Object) - Method in class net.sf.basedb.util.extensions.manager.FactoryParametersKey

equals(Object) - Method in class net.sf.basedb.util.extensions.manager.PluginInfoKey

equals(Object) - Method in class net.sf.basedb.util.extensions.Registry.AttributeKey

equals(Object) - Method in class net.sf.basedb.util.gtf.GtfInputStream.Attribute

equals(Object) - Method in class net.sf.basedb.util.jobagent.JobInfo

equals(Object) - Method in class net.sf.basedb.util.listable.TransformCache.CacheKey

equals(Object) - Method in class net.sf.basedb.util.overview.cache.DirectionalCacheKey

equals(Object) - Method in class net.sf.basedb.util.overview.cache.IndexedCacheKey

equals(Object) - Method in class net.sf.basedb.util.overview.Failure

One failure is the same as another if they have the same validator but different nodes referencing the same item with equal descriptors.

equals(Object) - Method in class net.sf.basedb.util.overview.validator.ExtractValidator.TagPosition

equals(Object) - Method in class net.sf.basedb.util.Tree

Equality only tests if the object is the same instance of this tree.

equals(Object) - Method in class net.sf.basedb.util.units.UnitCache.CacheKey

equals(Object, Object) - Static method in class net.sf.basedb.util.EqualsHelper

Check if two objects are equal according to their equals implementation.

EqualsConverter - Class in net.sf.basedb.util.jep.convert

Convert the '==' operator to a Query API Restriction.

EqualsConverter() - Constructor for class net.sf.basedb.util.jep.convert.EqualsConverter

EqualsFilter<T> - Class in net.sf.basedb.util.filter

A filter implementation that only accepts an object if it is equal (using Object.equals()) to a given object.

EqualsFilter(T) - Constructor for class net.sf.basedb.util.filter.EqualsFilter

Create a new filter.

EqualsHelper - Class in net.sf.basedb.util

Helper class for implementing equals and hash code calculations in classes.

EqualsHelper() - Constructor for class net.sf.basedb.util.EqualsHelper

EQUIVALENT_DOSE - Static variable in class net.sf.basedb.core.Quantity

The id for the Quantity object representing equivalent dose.

error - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemErrorColumn

error - Variable in class net.sf.basedb.core.SimpleProgressReporter

error - Variable in class net.sf.basedb.util.FileCopyRunnable

error(String) - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLogger

Log an ERROR message.

error(String, Throwable) - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLogger

Log an ERROR message with an optional stacktrace.

error(SAXParseException) - Method in class net.sf.basedb.util.XmlUtil2.Validator

Errors thrown with a detailed error message.

ERROR - Enum constant in enum class net.sf.basedb.core.Job.Status

The job has finished with an error.

ERROR - Enum constant in enum class net.sf.basedb.core.plugin.Response.Status

ERROR - Enum constant in enum class net.sf.basedb.util.extensions.logging.LogLevel

ERROR - Enum constant in enum class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory.Level

ERROR - Enum constant in enum class net.sf.basedb.util.overview.Severity

The rule generate errors.

ERROR_SECTION - Static variable in class net.sf.basedb.plugins.util.Parameters

The name of the parameter created by Parameters.errorSection(String, String).

errorClazz - Variable in class net.sf.basedb.clients.web.taglib.table.Cell

Optional class attribute for errors.

errorHandler - Variable in class net.sf.basedb.plugins.AbstractFlatFileImporter

errorHandler - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

errorHandler - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

errorHandler - Variable in class net.sf.basedb.util.extensions.ExtensionPointContext

ErrorHandler - Interface in net.sf.basedb.util.error

An interface to make it easier to implement dynamic error handling.

ErrorHandler<A extends Action> - Interface in net.sf.basedb.util.extensions

Error handlers are created by the factory for each request/use of an extension point.

errorHandlerFactory - Variable in class net.sf.basedb.util.extensions.ExtensionPointBean

errorHandlerFactory - Variable in class net.sf.basedb.util.extensions.ExtensionPointContext

errorHandlerFactory - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint

ErrorHandlerFactory<A extends Action> - Interface in net.sf.basedb.util.extensions

Error handler factories are responsible for creating error handlers.

errorHandlers - Variable in class net.sf.basedb.util.error.ClassMapErrorHandler

Map of registered error handlers.

errorIfNotFound - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter

errorIfNotFound - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

errorList - Variable in class net.sf.basedb.core.PluginResponse

errorMessage - Variable in class net.sf.basedb.core.data.FileSetMemberData

errors - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper

errors - Variable in class net.sf.basedb.util.fileset.ValidationRenderer

errorSection - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter

Section definition for grouping error handling options.

errorSection - Static variable in class net.sf.basedb.plugins.util.Parameters

Section definition for grouping error handling options.

errorSection(String, String) - Static method in class net.sf.basedb.plugins.util.Parameters

Create a parameter starting an error section.

escape(String) - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate

Replace newlines and tabs with a space.

escape(String) - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate

ESCAPE - Variable in class net.sf.basedb.core.migrate.ByteArrayWriter

ESCAPE - Variable in class net.sf.basedb.core.migrate.TextWriter

estimated - Variable in class net.sf.basedb.clients.jobagent.slotmanager.Slot

estimatedExecutionTime - Variable in class net.sf.basedb.core.data.JobData

estimatedExecutionTime - Variable in class net.sf.basedb.core.PluginResponse

evaluate(Annotatable) - Method in class net.sf.basedb.clients.web.extensions.list.RawDataTypeFilter

evaluate(Annotatable) - Method in class net.sf.basedb.clients.web.extensions.list.SubtypeFilter

evaluate(Annotatable) - Method in class net.sf.basedb.util.annotations.InheritAnnotationsManager.UsableParentFilter

evaluate(EntityQuery) - Method in class net.sf.basedb.core.query.ReturnClassFilter

Returns TRUE if the EntityQuery.getItemType() returns an item type whose Item.getItemClass() is compatible with the specified class.

evaluate(AnnotationSnapshot) - Method in class net.sf.basedb.clients.web.util.ProjectSpecificInfoFilter

Evaluate the annotation snapshot and update the flags if the snapshot is a project-specific annotation and overrides a default value.

evaluate(AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationFilter

evaluate(AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil

evaluate(AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationTypeFilter

evaluate(AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.DisabledInheritanceFilter

evaluate(AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.ProjectFilter

evaluate(AnnotationSnapshot) - Method in class net.sf.basedb.util.annotations.InheritAnnotationsManager.AnnotationTypeFilter

evaluate(AnnotationSnapshot) - Method in class net.sf.basedb.util.annotations.InheritSpecification

evaluate(ContextUtil.ContextResult) - Method in class net.sf.basedb.util.AutoDetectFileFormat.IsImportableFilter

evaluate(ContextUtil.ContextResult) - Method in class net.sf.basedb.util.ContextUtil.IsInContextFilter

evaluate(ExtensionsFile) - Method in class net.sf.basedb.clients.web.extensions.IgnoreFilter

evaluate(ExtensionsFile) - Method in class net.sf.basedb.clients.web.extensions.InstallFilter

evaluate(ExtensionsFile) - Method in class net.sf.basedb.clients.web.extensions.UninstallFilter

evaluate(ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.filter.DeletedFilter

evaluate(ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.filter.InstalledFilter

evaluate(ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.filter.InvalidAndModifiedFilter

evaluate(ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.filter.ValidAndNewOrModifiedFilter

evaluate(ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.filter.WasProcessedFilter

evaluate(Node) - Method in class net.sf.basedb.util.overview.filter.BasicItemFilter

evaluate(Node) - Method in class net.sf.basedb.util.overview.filter.HasAttributeFilter

evaluate(Node) - Method in class net.sf.basedb.util.overview.filter.ItemTypeFilter

evaluate(Node) - Method in class net.sf.basedb.util.overview.filter.NodeTypeFilter

evaluate(HttpResponse) - Method in class net.sf.basedb.util.GeoLocation.ResponseFilter

evaluate(Element) - Method in class net.sf.basedb.util.extensions.xml.ExtensionPointFilter

evaluate(Element) - Method in class net.sf.basedb.util.extensions.xml.PluginDefinitionFilter

evaluate(T) - Method in class net.sf.basedb.util.filter.AllOfFilter

evaluate(T) - Method in class net.sf.basedb.util.filter.EqualsFilter

evaluate(T) - Method in interface net.sf.basedb.util.filter.Filter

Evaluate if the given object should pass the filter or not.

evaluate(T) - Method in class net.sf.basedb.util.filter.IdentityFilter

evaluate(T) - Method in class net.sf.basedb.util.filter.InstanceOfFilter

evaluate(T) - Method in class net.sf.basedb.util.filter.InverseFilter

evaluate(T) - Method in class net.sf.basedb.util.filter.NoneOfFilter

evaluate(T) - Method in class net.sf.basedb.util.filter.NotNullFilter

evaluate(T) - Method in class net.sf.basedb.util.filter.OneOfFilter

evaluate(T) - Method in class net.sf.basedb.util.filter.StaticFilter

evaluateFormula(Cell) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo

evaluateFormulas - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil

evenodd - Variable in class net.sf.basedb.clients.web.taglib.table.Table

Keep track of which class to use for the next row.

event - Variable in class net.sf.basedb.core.data.BioMaterialEventSourceData

event - Variable in class net.sf.basedb.core.data.BioPlateEventParticipantData

eventDate - Variable in class net.sf.basedb.core.data.BioMaterialEventData

eventDate - Variable in class net.sf.basedb.core.data.BioPlateData

eventDate - Variable in class net.sf.basedb.core.data.BioPlateEventData

eventDate - Variable in class net.sf.basedb.core.data.PlateEventData

EventFilter - Interface in net.sf.basedb.util.extensions.events

A filter for events before they are sent to an EventHandler.

EventHandler - Interface in net.sf.basedb.util.bfs

Event handlers are used for reacting to various parsing events when parsing BFS files.

EventHandler - Interface in net.sf.basedb.util.extensions.events

An event handler receives events about things happening to extensions and extension points.

eventHandlers - Variable in class net.sf.basedb.util.extensions.Registry

eventParticipants - Variable in class net.sf.basedb.core.data.BioPlateData

events - Variable in class net.sf.basedb.core.data.BioPlateEventTypeData

events - Variable in class net.sf.basedb.core.data.MeasuredBioMaterialData

events - Variable in class net.sf.basedb.core.data.PlateData

eventType - Variable in class net.sf.basedb.core.data.BioMaterialEventData

eventType - Variable in class net.sf.basedb.core.data.BioPlateEventData

eventType - Variable in class net.sf.basedb.util.extensions.events.ExtensionEventFilter

EventType<T> - Class in net.sf.basedb.util.bfs

Defines an event type that is sent in event notifications to event handlers.

EventType - Class in net.sf.basedb.util.extensions.events

Represents different types of event.

EventType(String) - Constructor for class net.sf.basedb.util.bfs.EventType

Create a new event type object.

EventType(String) - Constructor for class net.sf.basedb.util.extensions.events.EventType

Create a new event type.

EventTypeFilter - Class in net.sf.basedb.util.extensions.events

Event filter that only passes on events of a specifiec event type.

EventTypeFilter(EventType) - Constructor for class net.sf.basedb.util.extensions.events.EventTypeFilter

Create a new event type filter.

eventTypes - Variable in class net.sf.basedb.core.data.PlateTypeData

EVERYONE - Static variable in class net.sf.basedb.core.Group

The id of the Everyone group where all users are (virtual) members.

EVERYONE - Static variable in class net.sf.basedb.core.Keyring

evict(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

evictData(Session, BasicData) - Static method in class net.sf.basedb.core.HibernateUtil

Remove a data item from the internal cache of Hibernate.

evictFromSecondLevelCacheIfModified - Variable in class net.sf.basedb.core.AnnotationBatcher

EvictPropertyPath(Type) - Constructor for class net.sf.basedb.core.Metadata.EvictPropertyPath

ExcelData(XlsxToCsvUtil.SheetInfo, int, int, int, String, String[], boolean, boolean, boolean) - Constructor for class net.sf.basedb.util.parser.FlatFileParser.ExcelData

Create a new data object.

excelFormatter - Variable in class net.sf.basedb.clients.web.plugins.ExportedProperty

ExcelFormatter<T,E> - Interface in net.sf.basedb.util.excel

Interface that is intended to be implemented by formatters that also want to support generating output for excel.

excelParsedLinesOffset - Variable in class net.sf.basedb.util.parser.FlatFileParser

The value of the parsedLines when the current Excel sheet is parsed.

excelSheet - Variable in class net.sf.basedb.util.parser.FlatFileParser

Excel sheet that is currently being parsed.

excelSheetName - Variable in class net.sf.basedb.util.parser.FlatFileParser

Name of the Excel sheet to parse if the file is an Excel file.

excelSheetParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter

Parameter definition for specifying the name of the sheet to use if the selected file is an Excel file.

ExcelValue<T> - Class in net.sf.basedb.util.excel

Represents a value and style format that should be written to a cell in an excel worksheet.

ExcelValue(T, String) - Constructor for class net.sf.basedb.util.excel.ExcelValue

ExcelValue.BlankValue<T> - Class in net.sf.basedb.util.excel

Represents a blank cell.

ExcelValue.BooleanValue - Class in net.sf.basedb.util.excel

Represents a cell with a numeric value.

ExcelValue.DateValue - Class in net.sf.basedb.util.excel

Represents a cell with a date value.

ExcelValue.IntValue - Class in net.sf.basedb.util.excel

Represents a cell with a numeric value without decimals.

ExcelValue.NumericValue - Class in net.sf.basedb.util.excel

Represents a cell with a numeric value.

ExcelValue.StringValue - Class in net.sf.basedb.util.excel

Represents a cell with a string value.

excelWorkbook - Variable in class net.sf.basedb.util.parser.FlatFileParser

Excel workbook that has been loaded.

exception - Variable in class net.sf.basedb.clients.web.fileupload.FileUploadProgress

exception - Variable in class net.sf.basedb.core.ItemContext

ExceptionCatcher - Class in net.sf.basedb.clients.web.taglib

This tag is a wrapper that catches any errors in it's body and outputs the error message.

ExceptionCatcher() - Constructor for class net.sf.basedb.clients.web.taglib.ExceptionCatcher

ExceptionInterruptHandler - Class in net.sf.basedb.core.signal

Interrupt handler implementation that always throw a SignalException.

ExceptionInterruptHandler(String) - Constructor for class net.sf.basedb.core.signal.ExceptionInterruptHandler

exclude - Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData

exclude(Collection<Include>) - Method in class net.sf.basedb.core.AbstractEntityQuery

exclude(Collection<Include>) - Method in interface net.sf.basedb.core.query.EntityQuery

exclude(Include...) - Method in class net.sf.basedb.core.AbstractEntityQuery

exclude(Include...) - Method in interface net.sf.basedb.core.query.EntityQuery

Specify options for which items to exclude from the result.

excludeDefaultValues - Variable in class net.sf.basedb.core.AnnotationRestriction.Options

excludeDefaultValues() - Method in class net.sf.basedb.core.AnnotationRestriction.Options

Should default values (for project-specific annotation types) be excluded from the query or not.

excludeLimit - Variable in class net.sf.basedb.util.IncludeExcludeFilter

execDirectory - Variable in class net.sf.basedb.plugins.Base1PluginExecuter

This is the directory where the plugin will generate its output.

execNameParameter - Variable in class net.sf.basedb.plugins.Base1PluginExecuter

The name of the executable.

execPathParameter - Static variable in class net.sf.basedb.plugins.Base1PluginExecuter

The path to where the plug-in executer can find the executables.

executable - Variable in enum class net.sf.basedb.core.Job.Status

execute(Connection) - Method in class net.sf.basedb.core.hibernate.DbIndexWork

execute(Connection) - Method in class net.sf.basedb.core.hibernate.ExecuteUpdateWork

From the Work interface -----------------------

execute(Connection) - Method in class net.sf.basedb.core.hibernate.GetCurrentCatalogWork

From the Work interface -----------------------

execute(Connection) - Method in class net.sf.basedb.core.hibernate.MultiUpdateWork

From the Work interface -----------------------

execute(Connection) - Method in class net.sf.basedb.core.hibernate.ResultSetWork

From the Work interface -----------------------

execute(Connection) - Method in class net.sf.basedb.core.hibernate.SavePointWork

From the Work interface -----------------------

execute(Connection) - Method in class net.sf.basedb.core.hibernate.SchemaExistsWork

From the Work interface -----------------------

execute(Connection) - Method in class net.sf.basedb.core.hibernate.SchemaGenerator

execute(Connection) - Method in class net.sf.basedb.core.hibernate.TableExistsWork

From the Work interface -----------------------

execute(Connection) - Method in class net.sf.basedb.core.hibernate.TableInfoWork

From the Work interface -----------------------

execute(Connection) - Method in class net.sf.basedb.core.MigrateRbaToDba

execute(Connection) - Method in class net.sf.basedb.core.Migration

execute(ProgressReporter, String) - Method in class net.sf.basedb.core.Job

Start the execution sequence for a job.

execute(ProgressReporter, String, String, JobAgentSettings) - Method in class net.sf.basedb.core.Job

Start the execution sequence for a job.

execute(ProgressReporter, String, JobAgentSettings) - Method in class net.sf.basedb.core.Job

EXECUTE_IMMEDIATELY - Enum constant in enum class net.sf.basedb.core.plugin.Response.Status

executeCommand - Variable in class net.sf.basedb.core.data.JobData

executeJob(SessionControl, Agent, Job, JobAgentSettings, Job.ExecutionTime) - Method in class net.sf.basedb.clients.jobagent.executors.DummyJobExecutor

executeJob(SessionControl, Agent, Job, JobAgentSettings, Job.ExecutionTime) - Method in class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor

executeJob(SessionControl, Agent, Job, JobAgentSettings, Job.ExecutionTime) - Method in class net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor

executeJob(SessionControl, Agent, Job, JobAgentSettings, Job.ExecutionTime) - Method in interface net.sf.basedb.clients.jobagent.JobExecutor

Execute the specified job.

executeQuery(PreparedStatement, SessionControl) - Static method in class net.sf.basedb.core.QueryExecutor

Execute a query by calling PreparedStatement.executeQuery().

executeUpdate() - Method in class net.sf.basedb.core.hibernate.QueryWrapper

executeUpdate(PreparedStatement, SessionControl) - Static method in class net.sf.basedb.core.QueryExecutor

Execute a query by calling PreparedStatement.executeUpdate().

executeUpdate(Query<?>) - Static method in class net.sf.basedb.core.HibernateUtil

Exceute an update or delete query.

ExecuteUpdateWork - Class in net.sf.basedb.core.hibernate

A JDBC work implementation that executes an update/insert/delete query and returns the number of rows that was affected by the query.

ExecuteUpdateWork(SessionControl, String) - Constructor for class net.sf.basedb.core.hibernate.ExecuteUpdateWork

Create a new work item.

EXECUTING - Enum constant in enum class net.sf.basedb.core.Job.Status

The job is executing.

ExecutionTime(int, String, int, int) - Constructor for enum class net.sf.basedb.core.Job.ExecutionTime

executor - Variable in class net.sf.basedb.plugins.executor.AbstractIOSupport

executorClass - Variable in class net.sf.basedb.clients.jobagent.Agent

existed - Variable in class net.sf.basedb.util.JarClassLoader.JarInfo

exists() - Method in class net.sf.basedb.core.ClonableProperty

Check if this cloned property still exists.

exists() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile

Check if the file exists.

exists(String) - Method in class net.sf.basedb.core.Presets

Check if a preset with the given name exists.

exists(String) - Static method in class net.sf.basedb.util.JarClassLoader

Check if a class loader for the given JAR file exists.

exists(String) - Method in class net.sf.basedb.util.StaticCache

Checks if a cache entry exists or not.

exists(String, boolean, boolean) - Method in class net.sf.basedb.core.ReporterBatcher

Check if a reporter with a given external id exists in the database or has been added to the batch queue of insertion.

exists(String, String, Item, EntityQuery) - Static method in class net.sf.basedb.core.query.AnyToAnyRestriction

Create a restriction that restrict a query to return items that has a linked item with the given link name.

exists(DbControl, BasicItem, String) - Static method in class net.sf.basedb.core.AnyToAny

Check if an item has a link with a given name.

exists(DbControl, Directory, String) - Static method in class net.sf.basedb.core.Directory

Checks if a subdirectory with the specified name exists in a directory.

exists(DbControl, Directory, String) - Static method in class net.sf.basedb.core.File

Checks if a file with the specified name exists in the directory.

exists(Session, Class<?>, int) - Static method in class net.sf.basedb.core.HibernateUtil

Checks if an item with the specified ID exists in the database.

existsInDb - Variable in class net.sf.basedb.core.dbengine.TableInfo

existsInDb() - Method in class net.sf.basedb.core.dbengine.TableInfo

Check if the table exists in the database or not.

exp(String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine

Return EXP(<value>).

exp(String) - Method in interface net.sf.basedb.core.dbengine.DbEngine

Get the function call that calculates the exponential of a value.

exp(Expression) - Static method in class net.sf.basedb.core.query.Expressions

Calculate the exponential of an expression: new expression = exp(e).

expand(Set<Permission>) - Static method in enum class net.sf.basedb.core.Permission

Expand the given set of permissions to make sure it includes all implicitely granted permissions.

expand(DbControl, Node, boolean) - Method in class net.sf.basedb.util.overview.GenericOverview

Load children of a node.

ExpConverter - Class in net.sf.basedb.util.jep.convert

Convert Exp function to a Query API Expression.

ExpConverter() - Constructor for class net.sf.basedb.util.jep.convert.ExpConverter

expectedNumBlocks - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter

experiment - Variable in class net.sf.basedb.clients.web.ExperimentExplorer

experiment - Variable in class net.sf.basedb.core.data.BioAssaySetData

experiment - Variable in class net.sf.basedb.core.data.JobData

experiment - Variable in class net.sf.basedb.core.data.ReporterListData

experiment - Variable in class net.sf.basedb.core.data.RootRawBioAssayData

experiment - Variable in class net.sf.basedb.core.data.TransformationData

experiment - Variable in class net.sf.basedb.core.data.VirtualDbData

experiment - Variable in class net.sf.basedb.core.ReporterCloneBatcher

The experiment this batcher inserts data for.

experiment - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter

Experiment - Class in net.sf.basedb.core

An experiment is the starting point of the analysis in BASE.

Experiment(ExperimentData) - Constructor for class net.sf.basedb.core.Experiment

Creates a new experiment item from the given data.

EXPERIMENT - Enum constant in enum class net.sf.basedb.core.Item

The item is an Experiment

EXPERIMENT - Static variable in class net.sf.basedb.core.QuotaType

The ID for experiments.

ExperimentalFactorLoader - Class in net.sf.basedb.util.overview.loader

Node loader implementation for experimental factors.

ExperimentalFactorLoader() - Constructor for class net.sf.basedb.util.overview.loader.ExperimentalFactorLoader

experimentalFactors - Variable in class net.sf.basedb.core.data.ExperimentData

ExperimentalFactorValidator - Class in net.sf.basedb.util.overview.validator

Validator implementation for experimental factors.

ExperimentalFactorValidator() - Constructor for class net.sf.basedb.util.overview.validator.ExperimentalFactorValidator

ExperimentData - Class in net.sf.basedb.core.data

Holds information about an experiment.

ExperimentData() - Constructor for class net.sf.basedb.core.data.ExperimentData

experimentDesign - Variable in class net.sf.basedb.core.data.ExperimentData

ExperimentExplorer - Class in net.sf.basedb.clients.web

A class for storing settings and doing work related to the experiment explorer tool in the web interface.

ExperimentExplorer(BioAssaySet) - Constructor for class net.sf.basedb.clients.web.ExperimentExplorer

Create a new experiment explorer.

ExperimentExplorer.AnnotationGroup - Class in net.sf.basedb.clients.web

An annotation group contains statistical information about the spot values falling into the group.

ExperimentExplorer.AnnotationSummary - Class in net.sf.basedb.clients.web

An annotation summary object keeps track of intensities and other statistical information based on the annotation group.

ExperimentExplorer.InExpression - Class in net.sf.basedb.clients.web

Creates a list of (numerical) values that can be used as the right-hand operand to the IN operator.

ExperimentExplorer.ReporterPositions - Class in net.sf.basedb.clients.web

Cache entry for a reporter with positions.

ExperimentExplorerPlotServlet - Class in net.sf.basedb.clients.web.servlet

Plot servlet for generating plots from experiment explorer.

ExperimentExplorerPlotServlet() - Constructor for class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet

ExperimentExplorerPlotServlet.ColumnKey - Class in net.sf.basedb.clients.web.servlet

Uses as a column key in the plots.

ExperimentLoader - Class in net.sf.basedb.util.overview.loader

Node loader implementation for experiments.

ExperimentLoader() - Constructor for class net.sf.basedb.util.overview.loader.ExperimentLoader

experimentParameter - Variable in class net.sf.basedb.plugins.IntensityCalculatorPlugin

experiments - Variable in class net.sf.basedb.core.data.AnnotationTypeData

experiments - Variable in class net.sf.basedb.core.data.RawBioAssayData

experimentType - Variable in class net.sf.basedb.core.data.ExperimentData

experimentType - Variable in class net.sf.basedb.plugins.IntensityCalculatorPlugin

ExperimentValidator - Class in net.sf.basedb.util.overview.validator

Validator implementation for experiments.

ExperimentValidator() - Constructor for class net.sf.basedb.util.overview.validator.ExperimentValidator

ExpExpression - Class in net.sf.basedb.core.query

Calculate the exponential of an expression: exp(e).

ExpExpression(Expression) - Constructor for class net.sf.basedb.core.query.ExpExpression

expirationDate - Variable in class net.sf.basedb.core.data.KitData

expirationDate - Variable in class net.sf.basedb.core.data.UserData

expirationDateColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.KitImporter

Column mapping parameter for the kit expiration date.

expirationDateMapper - Variable in class net.sf.basedb.plugins.batchimport.KitImporter

explicitClean() - Method in class net.sf.basedb.core.DbControl.State

Explicit cleanup of the DbControl is happening.

explorer - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary

exponent - Variable in class net.sf.basedb.core.query.PowerExpression

export - Variable in class net.sf.basedb.core.Migration

EXPORT - Enum constant in enum class net.sf.basedb.core.plugin.Plugin.MainType

exportable - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

exportable - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

exportable - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef

If the column is exportable or not

exportable - Variable in class net.sf.basedb.clients.web.taglib.table.TableColumn

ExportableField - Interface in net.sf.basedb.util.export.spotdata

Interface that represents an exportable field.

ExportableFieldConverter - Interface in net.sf.basedb.util.export.spotdata

Defines method for converting a string representation to an exportable assay or dynamic field that can be used with AbstractBioAssaySetExporter implementations.

ExportableFieldFactory - Class in net.sf.basedb.util.export.spotdata

Utility class with factory methods that helps with the creation of exportable fields.

ExportableFieldFactory() - Constructor for class net.sf.basedb.util.export.spotdata.ExportableFieldFactory

ExportableFieldFormatter - Class in net.sf.basedb.util.export.spotdata

Formatter implementation that formats an exportable field by returning the column title.

ExportableFieldFormatter() - Constructor for class net.sf.basedb.util.export.spotdata.ExportableFieldFormatter

Create a new formatter.

ExportableFieldFormatter(String) - Constructor for class net.sf.basedb.util.export.spotdata.ExportableFieldFormatter

Create a new formatter.

exportableFields - Variable in class net.sf.basedb.plugins.BaseFileExporterPlugin

exportableFields - Variable in class net.sf.basedb.plugins.BfsExporterPlugin

exportAll(String, ProgressReporter) - Static method in class net.sf.basedb.core.Migration

Export the current BASE database to data files in the directory on the given path.

exportAssayAnnotations() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter

Export the assay annotations.

exportAssaysSectionData() - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter

Export data for the 'assays' section that contains information about the bioassays in the source bioassay set.

exportAssaysSectionHeaders() - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter

Exports headers for the 'assays' section which contains metadata information about the assays in the bioassay set.

exportCompressed - Variable in class net.sf.basedb.core.Migration

exportContext - Variable in class net.sf.basedb.clients.web.extensions.list.ListColumnExportRenderer

exportData(DbControl, Directory, ProgressReporter) - Method in class net.sf.basedb.plugins.Base1PluginExecuter

Export the bioassay set to a file called 'stdin.txt' in the plugin directory.

exportedPositions - Variable in class net.sf.basedb.util.export.spotdata.BfsExporter

ExportedProperty - Class in net.sf.basedb.clients.web.plugins

ExportedProperty(String, String, Metadata.PropertyPath, AnnotationType, boolean, Unit, Formatter, ExcelFormatter, DataLoader) - Constructor for class net.sf.basedb.clients.web.plugins.ExportedProperty

exporter - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

exportFormatter - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

exportFormatterClass - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

exportGal(DbControl, ArrayDesign, Integer, PrintWriter, ProgressReporter) - Method in class net.sf.basedb.plugins.GalExporter

Exports an array design with features to a GAL file.

exportGlobalFooter() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

Export global footer or other data that only appears once in the end of the exported file.

exportGlobalFooter() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter

Exports reporter annotations.

exportGlobalHeader() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

Export global headers or other data that only appear once in the beginning of the exported file.

exportGlobalHeader() - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter

Export 'settings' and 'assays' sections.

exportGlobalHeader() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter

Export the metadata and assay annotations.

exportMetadata() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter

Export the metadata file which contains information about the other files (reporter annotations, assay annotations and spot data), plug-in parameters, etc.

ExportOutputStream - Class in net.sf.basedb.core.plugin

An output stream used for immediate download from export plugins.

ExportOutputStream(OutputStream) - Constructor for class net.sf.basedb.core.plugin.ExportOutputStream

Create a new export stream.

exportPath - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory.PropertyPathAction

exportProperties(DbControl, ExportOutputStream, String, String, List<ExportedProperty>, Item, Query, ProgressReporter) - Method in class net.sf.basedb.clients.web.plugins.SimpleExport

Exports properties from a query to an output stream.

exportProperty - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

exportProperty - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

exportProperty - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef

Optional property used for exporting.

exportReporterAnnotations(ProgressReporter, long) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter

Export the reporter annotations.

exportSectionData() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

Export section data.

exportSectionData() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter

Export all spot data.

exportSectionData() - Method in class net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter

Exports data for all bioassays in a single 'spots' section.

exportSectionData() - Method in class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter

Exports data for the current bioassay in a 'spots' section.

exportSectionFooter() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

End the section by exporting a footer.

exportSectionFooter() - Method in class net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter

Ends the 'spots' section.

exportSectionFooter() - Method in class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter

Ends the current 'spots' section.

exportSectionHeader() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

Start a new section in the export by exporting section headers.

exportSectionHeader() - Method in class net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter

Exports headers for a single 'spots' section.

exportSectionHeader() - Method in class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter

Exports headers for a 'spots' section, and make preparations for the current data section (one section per bioassay).

exportSettingsSection() - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter

Export the settings section which contains all parameter values registered with BaseFileExporter.setParameter(String, String).

exportSpotData(ProgressReporter, long) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter

Export spot data.

exportSpotSectionData(List<BioAssay>, DynamicSpotQuery, ProgressReporter, long) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter

Export the spot data of a 'spot' section.

exportSpotSectionHeaders(List<BioAssay>, long) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter

Start a new 'spot' section and export the standard headers: 'channels, 'assays', 'columns', 'assayFields' and 'count'.

exportStream - Variable in class net.sf.basedb.clients.web.plugins.PlainTextTemplate

exportStream - Variable in class net.sf.basedb.clients.web.plugins.XMLTemplate

ExportTemplate - Interface in net.sf.basedb.clients.web.plugins

A helper interface for the SimpleExport class to make it easier to output exported data in different formats.

exportTitle - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

exportTitle - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef

Alternate title to use when exporting.

expression - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

expression - Variable in class net.sf.basedb.core.query.AscOrder

expression - Variable in class net.sf.basedb.core.query.DescOrder

expression - Variable in class net.sf.basedb.core.query.HqlExpression

The restriction or expression as a string.

expression - Variable in class net.sf.basedb.core.query.VirtualColumnExpression.WrappedExpression

expression - Variable in class net.sf.basedb.util.export.spotdata.SimpleDynamicField

expression - Variable in class net.sf.basedb.util.parser.JepMapper

expression(String, String) - Static method in class net.sf.basedb.core.query.Hql

expression(String, AnnotationType) - Static method in class net.sf.basedb.core.query.Annotations

Create an expression representing the value of an annotation to a joined item of the query.

expression(AnnotationType) - Static method in class net.sf.basedb.core.query.Annotations

Create an expression representing the value of an annotation to the root item of the query.

expression(Expression, String) - Static method in class net.sf.basedb.core.query.Selects

Same as expression(e1, alias, false).

expression(Expression, String, boolean) - Static method in class net.sf.basedb.core.query.Selects

Create a selection from an expression, optionally giving it an alias.

Expression - Interface in net.sf.basedb.core.query

An expression query element.

expressionOperator - Variable in enum class net.sf.basedb.core.Operator

expressionParameter - Static variable in class net.sf.basedb.plugins.JepExtraValueCalculator

expressions - Variable in class net.sf.basedb.core.IntensityFormula

Expressions - Class in net.sf.basedb.core.query

A factory class to create expressions.

Expressions() - Constructor for class net.sf.basedb.core.query.Expressions

ExpressionSelect - Class in net.sf.basedb.core.query

A selection query element that selects an expression, optionally giving it an alias.

ExpressionSelect(Expression, String, boolean) - Constructor for class net.sf.basedb.core.query.ExpressionSelect

ExtendableData - Interface in net.sf.basedb.core.data

This class is inherited by data classes that supports per-server additions of columns to the underlying database table.

extended - Variable in class net.sf.basedb.core.authentication.ExtraUserInformation

ExtendedAbout - Interface in net.sf.basedb.util.extensions

Adds extra information to the About interface.

ExtendedDynamicField(String, boolean, DynamicField) - Constructor for class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField

ExtendedDynamicField(String, String, boolean, DynamicField) - Constructor for class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField

ExtendedExportableField(String, boolean, ExportableField) - Constructor for class net.sf.basedb.plugins.BfsExporterPlugin.ExtendedExportableField

ExtendedExportableField(String, String, boolean, ExportableField) - Constructor for class net.sf.basedb.plugins.BfsExporterPlugin.ExtendedExportableField

extendedMappers - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

extendedMappers - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

extendedProperties - Variable in class net.sf.basedb.core.data.RawData

extendedProperties - Variable in class net.sf.basedb.core.data.ReporterData

extendedProperties - Variable in class net.sf.basedb.core.data.UserData

extendedProperties - Variable in class net.sf.basedb.core.ReporterBatcher

The extended properties for reporters

ExtendedProperties - Class in net.sf.basedb.core

This class is used for reading XML files with information about extended properties.

ExtendedProperties() - Constructor for class net.sf.basedb.core.ExtendedProperties

extendedPropertiesFile - Static variable in class net.sf.basedb.core.Application

The path to the file containing extended properties.

extendedProperty - Variable in class net.sf.basedb.core.data.ReporterClonePropertyData

ExtendedProperty - Class in net.sf.basedb.core

Holds information about an extended property for a class.

ExtendedProperty(String, String, String, String, Type, int, boolean, boolean, boolean, boolean, boolean, Formula.AverageMethod, List<ExtendedPropertyLinker>) - Constructor for class net.sf.basedb.core.ExtendedProperty

Create a new extended property.

ExtendedPropertyAccessor - Class in net.sf.basedb.core

This class is used to interface with Hibernate for extended properties.

ExtendedPropertyAccessor() - Constructor for class net.sf.basedb.core.ExtendedPropertyAccessor

Create a new ExtendedPropertyAccessor object.

ExtendedPropertyAccessor.GetterSetter - Class in net.sf.basedb.core

This class implements the Hibernate Getter and Setter interfaces.

ExtendedPropertyFormatter<T> - Class in net.sf.basedb.clients.web.formatter

Formatter for extended property values.

ExtendedPropertyFormatter(ExtendedProperty, Formatter<T>) - Constructor for class net.sf.basedb.clients.web.formatter.ExtendedPropertyFormatter

Create an extended property formatter.

ExtendedPropertyLinker - Class in net.sf.basedb.core

Used to create links from extended property values.

ExtendedPropertyLinker(String, String) - Constructor for class net.sf.basedb.core.ExtendedPropertyLinker

extension - Variable in class net.sf.basedb.core.data.DataFileTypeData

extension - Variable in class net.sf.basedb.core.data.MimeTypeData

extension - Variable in class net.sf.basedb.util.extensions.ExtensionContext

Extension<A extends Action> - Interface in net.sf.basedb.util.extensions

Represents a concrete implementation of an extension to an extension point.

EXTENSION_COMPARATOR - Static variable in class net.sf.basedb.util.extensions.Registry

Comparator that sort extensions according to their names.

EXTENSION_ID_COMPARATOR - Static variable in class net.sf.basedb.util.extensions.Registry

Comparator that sort extensions according to their ids.

EXTENSION_KEY - Static variable in class net.sf.basedb.clients.web.extensions.JspContext

The key that is used when storing an Extension object in a request/page/session/etc. attribute.

EXTENSION_POINT_ID - Static variable in class net.sf.basedb.clients.web.extensions.service.Services

EXTENSION_POINT_ID - Static variable in class net.sf.basedb.util.uri.ConnectionManagerUtil

The ID of the connection manager extension point.

ExtensionBean<A extends Action> - Class in net.sf.basedb.util.extensions

A bean-like implementation of the Extension interface.

ExtensionBean() - Constructor for class net.sf.basedb.util.extensions.ExtensionBean

Create a new empty extension bean.

ExtensionBean(String, String, float, About, ActionFactory<? extends A>, RendererFactory<? super A>) - Constructor for class net.sf.basedb.util.extensions.ExtensionBean

Create a new fully initialised extension bean.

ExtensionCells - Class in net.sf.basedb.clients.web.taglib.table

Tag for generating content from extension columns.

ExtensionCells() - Constructor for class net.sf.basedb.clients.web.taglib.table.ExtensionCells

ExtensionChildNodeLoader<I> - Class in net.sf.basedb.util.overview.loader

Wrapper for node loaders that automatically hooks into the extension system when loading child nodes for a parent node.

ExtensionChildNodeLoader(NodeLoader<I>) - Constructor for class net.sf.basedb.util.overview.loader.ExtensionChildNodeLoader

Wrap the given parent node loader.

extensionColumns - Variable in class net.sf.basedb.clients.web.taglib.table.ExtensionCells

extensionColumns - Variable in class net.sf.basedb.clients.web.taglib.table.Table

ExtensionContext<A extends Action> - Class in net.sf.basedb.util.extensions

Invokation context for an extension.

ExtensionContext(ExtensionPointContext<A>, Registry.RegisteredExtension<A>) - Constructor for class net.sf.basedb.util.extensions.ExtensionContext

ExtensionEventFilter - Class in net.sf.basedb.util.extensions.events

Event filter that only passes events for a specific extension.

ExtensionEventFilter(String, EventType) - Constructor for class net.sf.basedb.util.extensions.events.ExtensionEventFilter

Create a new extension event filter.

ExtensionEventFilter(Extension<?>, EventType) - Constructor for class net.sf.basedb.util.extensions.events.ExtensionEventFilter

Create a new extension event filter.

extensionId - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

extensionId - Variable in class net.sf.basedb.clients.web.extensions.service.DummyService

extensionId - Variable in class net.sf.basedb.clients.web.taglib.extensions.Scripts

extensionId - Variable in class net.sf.basedb.clients.web.taglib.extensions.Stylesheets

extensionId - Variable in class net.sf.basedb.util.extensions.logging.ExtensionsLog

extensionIsRegistered(String) - Method in class net.sf.basedb.util.extensions.Registry

Checks if an extension is registered or not.

ExtensionKey - Class in net.sf.basedb.util.extensions.manager

Key implementation used to identify extensions.

ExtensionKey(String) - Constructor for class net.sf.basedb.util.extensions.manager.ExtensionKey

Create a new key for an extension with the given id.

ExtensionKey(Extension<?>) - Constructor for class net.sf.basedb.util.extensions.manager.ExtensionKey

Create a new key for an extension.

ExtensionNodeValidator<I> - Class in net.sf.basedb.util.overview.validator

Wrapper for node validators that hooks into the extension system when validating nodes.

ExtensionNodeValidator(NodeValidator<I>, Object) - Constructor for class net.sf.basedb.util.overview.validator.ExtensionNodeValidator

Wrap the given parent node validator.

extensionPoint - Variable in class net.sf.basedb.util.extensions.ExtensionBean

extensionPoint - Variable in class net.sf.basedb.util.extensions.ExtensionPointContext

extensionPoint - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtension

ExtensionPoint<A extends Action> - Interface in net.sf.basedb.util.extensions

An extension point is a place, defined by a client application, that can be extended.

EXTENSIONPOINT_COMPARATOR - Static variable in class net.sf.basedb.util.extensions.Registry

Comparator that sort extension points according to their names.

EXTENSIONPOINT_ID_COMPARATOR - Static variable in class net.sf.basedb.util.extensions.Registry

Comparator that sort extensions according to their ids.

ExtensionPointBean<A extends Action> - Class in net.sf.basedb.util.extensions

A bean-like implementation of the ExtensionPoint interface.

ExtensionPointBean() - Constructor for class net.sf.basedb.util.extensions.ExtensionPointBean

Create a new empty extension point bean.

ExtensionPointBean(String, String, String, Class<A>, RendererFactory<A>, boolean) - Constructor for class net.sf.basedb.util.extensions.ExtensionPointBean

Create a new fully initialised extension point bean.

ExtensionPointContext<A extends Action> - Class in net.sf.basedb.util.extensions

Invokation context for an extension point.

ExtensionPointContext(Registry, ClientContext, Registry.RegisteredExtensionPoint<A>, ErrorHandlerFactory<? super A>) - Constructor for class net.sf.basedb.util.extensions.ExtensionPointContext

ExtensionPointEventFilter - Class in net.sf.basedb.util.extensions.events

Event filter that only passes events for a specific extension point.

ExtensionPointEventFilter(String) - Constructor for class net.sf.basedb.util.extensions.events.ExtensionPointEventFilter

Create a new extension point event filter

ExtensionPointEventFilter(ExtensionPoint<?>) - Constructor for class net.sf.basedb.util.extensions.events.ExtensionPointEventFilter

Create a new extension point event filter.

ExtensionPointFilter - Class in net.sf.basedb.util.extensions.xml

Filter implementation that can be used to match extension points and extensions based on the ID of the extension point.

ExtensionPointFilter(String) - Constructor for class net.sf.basedb.util.extensions.xml.ExtensionPointFilter

Create a new filter based on the given pattern.

ExtensionPointFilter(Pattern) - Constructor for class net.sf.basedb.util.extensions.xml.ExtensionPointFilter

Create a new filter based on the given pattern.

extensionPointId - Variable in class net.sf.basedb.core.signal.ExtensionSignalTransporter

extensionPointIsRegistered(String) - Method in class net.sf.basedb.util.extensions.Registry

Checks if an extension point is registered or not.

ExtensionPointKey - Class in net.sf.basedb.util.extensions.manager

Key implementation used to identify extension points.

ExtensionPointKey(String) - Constructor for class net.sf.basedb.util.extensions.manager.ExtensionPointKey

Create a new key for an extension point with the given id.

ExtensionPointKey(ExtensionPoint<?>) - Constructor for class net.sf.basedb.util.extensions.manager.ExtensionPointKey

Create a new key for an extension point.

extensionPoints - Variable in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor.FileData

extensionPoints - Variable in class net.sf.basedb.util.extensions.Registry

extensionPoints - Variable in class net.sf.basedb.util.extensions.xml.XmlLoader

extensions - Variable in class net.sf.basedb.clients.web.taglib.extensions.Render

extensions - Variable in class net.sf.basedb.clients.web.taglib.tab.TabControl

extensions - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef

extensions - Static variable in class net.sf.basedb.plugins.Bzip2FileUnpacker

extensions - Static variable in class net.sf.basedb.plugins.GzipFileUnpacker

extensions - Static variable in class net.sf.basedb.plugins.TarFileUnpacker

extensions - Static variable in class net.sf.basedb.plugins.ZipFileUnpacker

extensions - Variable in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor.FileData

extensions - Variable in class net.sf.basedb.util.extensions.Registry

extensions - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint

extensions - Variable in class net.sf.basedb.util.extensions.xml.XmlLoader

ExtensionsControl - Class in net.sf.basedb.clients.web.extensions

Controller class for the extension system in the web client.

ExtensionsControl(DbControl, Set<Permission>) - Constructor for class net.sf.basedb.clients.web.extensions.ExtensionsControl

ExtensionsFile - Class in net.sf.basedb.util.extensions.manager

Represents a file with extensions in it.

ExtensionsFile(ExtensionsManager, File) - Constructor for class net.sf.basedb.util.extensions.manager.ExtensionsFile

Create a new extensions file backed by a real file on the file system.

ExtensionsFile(ExtensionsManager, File, boolean) - Constructor for class net.sf.basedb.util.extensions.manager.ExtensionsFile

Create a new extensions file backed by a real file on the file system.

ExtensionsFile(ExtensionsManager, File, URI, String, boolean) - Constructor for class net.sf.basedb.util.extensions.manager.ExtensionsFile

ExtensionsFile(ExtensionsManager, URI) - Constructor for class net.sf.basedb.util.extensions.manager.ExtensionsFile

Create a new extension file backed by an URI.

ExtensionsFile.WriteableExtensionsFile - Class in net.sf.basedb.util.extensions.manager

An extensions file with additional methods that allows adding or modifying information in the underlying extensions file.

ExtensionsFileProcessor - Interface in net.sf.basedb.util.extensions.manager

Interface that is used to request a callback for each extensions file managed by an extensions manager.

ExtensionsFilter - Interface in net.sf.basedb.util.extensions

Allows extensions and extension points to be enabled/disabled and sorted externally.

ExtensionSignalTransporter - Class in net.sf.basedb.core.signal

A signal transporter implementation send all signals to extensions extending the "net.sf.basedb.core.signal" extension point.

ExtensionSignalTransporter() - Constructor for class net.sf.basedb.core.signal.ExtensionSignalTransporter

ExtensionSignalTransporter.SendSignalRenderer - Class in net.sf.basedb.core.signal

ExtensionsInvoker<A extends Action> - Class in net.sf.basedb.util.extensions

Object of this class handles a single invokation of the extensions for one or several extension points.

ExtensionsInvoker(ClientContext, Collection<ExtensionContext<A>>) - Constructor for class net.sf.basedb.util.extensions.ExtensionsInvoker

Creates a new invoker object.

extensionsJar - Variable in class net.sf.basedb.clients.web.extensions.XJspCompiler

ExtensionsLog - Class in net.sf.basedb.util.extensions.logging

Instances hold the log entries for a single extension.

ExtensionsLog(String) - Constructor for class net.sf.basedb.util.extensions.logging.ExtensionsLog

ExtensionsLogger - Class in net.sf.basedb.util.extensions.logging

A simple logger that services can use to send log message to the BASE core.

ExtensionsLogger(ExtensionsLog) - Constructor for class net.sf.basedb.util.extensions.logging.ExtensionsLogger

ExtensionsLogger(ExtensionsLog, Logger) - Constructor for class net.sf.basedb.util.extensions.logging.ExtensionsLogger

ExtensionsManager - Class in net.sf.basedb.util.extensions.manager

An extensions manager is responsible for handling a group of extensions in the form of files stored in the file system.

ExtensionsManager(Registry, File) - Constructor for class net.sf.basedb.util.extensions.manager.ExtensionsManager

Create a new extensions manager and use the given registry to store extensions.

ExtensionsManager.JarFirstURIComparator - Class in net.sf.basedb.util.extensions.manager

Compare URI:s so that 'jar:' scheme always are listed first.

ExtensionsServlet - Class in net.sf.basedb.clients.web.servlet

This servlet is acting as a proxy for requests to extension defined servlets.

ExtensionsServlet() - Constructor for class net.sf.basedb.clients.web.servlet.ExtensionsServlet

ExtensionsUtil - Class in net.sf.basedb.util.extensions

Utility class collecting some useful functions related to extensions.

ExtensionsUtil() - Constructor for class net.sf.basedb.util.extensions.ExtensionsUtil

EXTERNAL - Enum constant in enum class net.sf.basedb.core.Location

The item is stored externally.

EXTERNAL - Static variable in class net.sf.basedb.core.authentication.AuthenticationMethod

This is a generic external authentication method.

EXTERNAL_ID - Static variable in class net.sf.basedb.core.ClonableProperty

The property name of the "static" property ReporterData.getExternalId().

EXTERNAL_ID - Static variable in class net.sf.basedb.plugins.batchimport.PropertyIdMethod

Use the external ID for finding items.

externalId - Variable in class net.sf.basedb.clients.jobagent.Agent

externalId - Variable in class net.sf.basedb.core.authentication.AuthenticatedUser

externalId - Variable in class net.sf.basedb.core.data.AnnotationTypeData

externalId - Variable in class net.sf.basedb.core.data.BioMaterialData

externalId - Variable in class net.sf.basedb.core.data.BioPlateData

externalId - Variable in class net.sf.basedb.core.data.ClientData

externalId - Variable in class net.sf.basedb.core.data.DataFileTypeData

externalId - Variable in class net.sf.basedb.core.data.ExtraValueTypeData

externalId - Variable in class net.sf.basedb.core.data.FeatureData

externalId - Variable in class net.sf.basedb.core.data.HelpData

externalId - Variable in class net.sf.basedb.core.data.ItemListData

externalId - Variable in class net.sf.basedb.core.data.JobAgentData

externalId - Variable in class net.sf.basedb.core.data.JobData

externalId - Variable in class net.sf.basedb.core.data.PlatformData

externalId - Variable in class net.sf.basedb.core.data.PlatformVariantData

externalId - Variable in class net.sf.basedb.core.data.ProtocolData

externalId - Variable in class net.sf.basedb.core.data.ReporterData

externalId - Variable in class net.sf.basedb.core.data.ReporterListData

externalId - Variable in class net.sf.basedb.core.data.UserData

externalId - Variable in class net.sf.basedb.core.RawDataBatcher.ReporterProxy

externalId - Variable in class net.sf.basedb.core.SessionControl.ClientInfo

externalIdColumnMapping - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

externalIdColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

externalIdIsUsed(DbControl, String) - Static method in class net.sf.basedb.core.User

Check if an external ID already exists in the database

externalIdMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

externalIdMapper - Variable in class net.sf.basedb.plugins.batchimport.BioSourceImporter

externalIdMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter

externalIdMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter

externalIndex - Variable in class net.sf.basedb.util.importer.spotdata.PositionEventHandler

ExternalProgramExecutor - Class in net.sf.basedb.plugins.executor

ExternalProgramExecutor() - Constructor for class net.sf.basedb.plugins.executor.ExternalProgramExecutor

ExternalProgramExecutor.RequestWrapper - Class in net.sf.basedb.plugins.executor

ExternalProgramExecutor.ResponseWrapper - Class in net.sf.basedb.plugins.executor

externalReporterId - Variable in class net.sf.basedb.core.RawDataBatcher.FeatureInfo

externalWorkbook - Variable in class net.sf.basedb.util.excel.XlsxTableWriter

EXTRA - Static variable in class net.sf.basedb.core.VirtualColumn

This column stores the data cube extra value number.

EXTRA_FLOAT - Static variable in class net.sf.basedb.core.VirtualColumn

This column stores extra float values.

EXTRA_INT - Static variable in class net.sf.basedb.core.VirtualColumn

This column stores extra integer values.

EXTRA_STRING - Static variable in class net.sf.basedb.core.VirtualColumn

This column stores extra string values.

EXTRA_VALUE_INNER - Static variable in class net.sf.basedb.core.DynamicPositionQueryJoiners

This instance joins extra values with an inner join.

EXTRA_VALUE_INNER - Static variable in class net.sf.basedb.core.DynamicSpotQueryJoiners

This instance joins extra values with an inner join.

EXTRA_VALUE_LEFT - Static variable in class net.sf.basedb.core.DynamicPositionQueryJoiners

This instance joins extra values with a left join.

EXTRA_VALUE_LEFT - Static variable in class net.sf.basedb.core.DynamicSpotQueryJoiners

This instance joins extra values with a left join.

extract - Variable in class net.sf.basedb.core.data.DerivedBioAssayData

extract - Variable in class net.sf.basedb.core.data.RawBioAssayData

extract - Variable in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper

Extract - Class in net.sf.basedb.core

This class is used to represent extract items.

Extract(ExtractData) - Constructor for class net.sf.basedb.core.Extract

EXTRACT - Enum constant in enum class net.sf.basedb.core.Item

The item is an Extract.

EXTRACT - Static variable in class net.sf.basedb.util.overview.NodeAttribute

Store a reference to an extract on a node.

EXTRACT_PATH - Static variable in class net.sf.basedb.util.overview.NodeAttribute

Store the ID values of extracts that should be followed on upstream paths as long as the current extract is not among one of the given parent extracts.

extractAndCreateRawBioAssays(DbControl, List<String>, boolean, File) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter

Extract array names and raw data property names from the column headers.

extractColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

extractColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

ExtractData - Class in net.sf.basedb.core.data

This represents an extract.

ExtractData() - Constructor for class net.sf.basedb.core.data.ExtractData

extractHasBeenSet - Variable in class net.sf.basedb.core.DerivedBioAssay

extractId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba

ExtractImporter - Class in net.sf.basedb.plugins.batchimport

Plug-in for importing extract items in a batch.

ExtractImporter() - Constructor for class net.sf.basedb.plugins.batchimport.ExtractImporter

EXTRACTION - Static variable in class net.sf.basedb.core.Kit

The ID for the extraction kit type, for example a kit used when creating an Extract from a Sample.

EXTRACTION - Static variable in class net.sf.basedb.core.Protocol

The ID for the extraction protocol type, for example a protocol used when creating an Extract from a Sample.

ExtractLoader - Class in net.sf.basedb.util.overview.loader

Node loader implementation for extracts.

ExtractLoader() - Constructor for class net.sf.basedb.util.overview.loader.ExtractLoader

extractMapper - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

extractMapper - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

ExtractNameGenerator - Class in net.sf.basedb.util.overview.node

Name generator implementation for Extract items.

ExtractNameGenerator(String, String) - Constructor for class net.sf.basedb.util.overview.node.ExtractNameGenerator

Create a new name generator.

extractPositionColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter

extractPositionMapper - Variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter

extractQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

ExtractResourcesProcessor - Class in net.sf.basedb.util.extensions.manager.processor

A file processor implementation that extracts resources from JAR files.

ExtractResourcesProcessor(File, Pattern, String, ProcessResults) - Constructor for class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor

Create a new processor.

ExtractResourcesProcessor(File, ProcessResults) - Constructor for class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor

Create a new processor.

extractsInChain - Variable in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper

ExtractToChildExtractTransformer - Class in net.sf.basedb.util.listable

Source item transformer implementation that transform extract items to their child extract items.

ExtractToChildExtractTransformer(boolean) - Constructor for class net.sf.basedb.util.listable.ExtractToChildExtractTransformer

Create a new extract to child extract transformer.

ExtractToChildExtractTransformer(boolean, boolean) - Constructor for class net.sf.basedb.util.listable.ExtractToChildExtractTransformer

Create a new extract to child extract transformer that only load children has a subtype with "push annotations" set.

ExtractToParentExtractTransformer - Class in net.sf.basedb.util.listable

Source item transformer implementation that transform extract items to their parent extract items.

ExtractToParentExtractTransformer(boolean) - Constructor for class net.sf.basedb.util.listable.ExtractToParentExtractTransformer

Create a new extract to parent extract transformer.

ExtractToParentExtractTransformer(boolean, boolean) - Constructor for class net.sf.basedb.util.listable.ExtractToParentExtractTransformer

Create a new extract to parent extract transformer that only load parents to extracts that has a subtype with "push annotations" set.

ExtractToParentExtractTransformer(boolean, CollectExtracts) - Constructor for class net.sf.basedb.util.listable.ExtractToParentExtractTransformer

Create a new extract to parent extract transformer that is considering extracts collected on downstream derived and raw bioassays.

ExtractToPhysicalBioAssayTransformer - Class in net.sf.basedb.util.listable

Source item transformer implementation that transform extract items to physical bioassays.

ExtractToPhysicalBioAssayTransformer() - Constructor for class net.sf.basedb.util.listable.ExtractToPhysicalBioAssayTransformer

Create a new extract to physical bioassay transformer.

ExtractToSampleTransformer - Class in net.sf.basedb.util.listable

Source item transformer that transform extract items to their parent samples.

ExtractToSampleTransformer() - Constructor for class net.sf.basedb.util.listable.ExtractToSampleTransformer

ExtractToSampleTransformer(boolean) - Constructor for class net.sf.basedb.util.listable.ExtractToSampleTransformer

Create a new extract to sample transformer that only load parent samples to extracts that has a subtype with "push annotations" set.

ExtractValidator - Class in net.sf.basedb.util.overview.validator

Validator implementation for extracts.

ExtractValidator() - Constructor for class net.sf.basedb.util.overview.validator.ExtractValidator

ExtractValidator.TagPosition - Class in net.sf.basedb.util.overview.validator

extraField - Variable in class net.sf.basedb.clients.web.extensions.login.LoginFormBean

extraFileImporter - Variable in class net.sf.basedb.util.importer.spotdata.BfsImporter

ExtraFileImporter - Interface in net.sf.basedb.util.bfs

Implementors are responsible for importing extra files specified in the BFS metadata file into the BASE file system.

extraFiles - Variable in class net.sf.basedb.util.export.spotdata.BfsExporter

extraFilter - Variable in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil

ExtraFloatParser - Class in net.sf.basedb.util.importer.spotdata

Parser that is responsible for extracting extra float values from the 'spot' section in a BASEfile.

ExtraFloatParser(String, int) - Constructor for class net.sf.basedb.util.importer.spotdata.ExtraFloatParser

Creates a new extra value parser.

extraFloats - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo

extraFloats - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo

extraInfo - Variable in class net.sf.basedb.core.authentication.AuthenticatedUser

extraNo - Variable in class net.sf.basedb.core.data.DataCubeExtraValueData

extraQuery - Variable in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter

extraSql - Variable in class net.sf.basedb.core.PositionExtraValueBatcher

The statement that inserts spot data.

extraSql - Variable in class net.sf.basedb.core.SpotExtraValueBatcher

The statement that inserts spot data.

extraSqlStatement - Variable in class net.sf.basedb.core.PositionExtraValueBatcher

The SQL string for the PositionExtraValueBatcher.extraSql statement.

extraSqlStatement - Variable in class net.sf.basedb.core.SpotExtraValueBatcher

The SQL string for the SpotExtraValueBatcher.extraSql statement.

extraToIndex - Variable in class net.sf.basedb.util.jep.ExtraValueFunction

ExtraUserInformation - Class in net.sf.basedb.core.authentication

Class for holding extra information about a user.

ExtraUserInformation() - Constructor for class net.sf.basedb.core.authentication.ExtraUserInformation

Creates a new ExtraUserInformation object.

extraValue - Variable in class net.sf.basedb.core.ExtraValueExpression

extraValue - Variable in class net.sf.basedb.core.ExtraValueJoin

extraValue - Variable in class net.sf.basedb.core.PositionExtraValueBatcher

The extra value object which links the extra value type.

extraValue - Variable in class net.sf.basedb.core.SpotExtraValueBatcher

The extra value object which links the extra value type.

extraValue(ExtraValue) - Static method in class net.sf.basedb.core.query.Dynamic

Create an expression representing the extra value of a spot or position.

extraValue(ExtraValueType, String, Formatter<?>) - Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory

Create a JEP dynamic field that exports an extra value.

extraValue(Type) - Static method in class net.sf.basedb.core.VirtualColumn

Get a column that stores the calculated extra values for a value type.

ExtraValue - Class in net.sf.basedb.core

Represents extra values attached to a BioAssaySet.

ExtraValue(ExtraValueData) - Constructor for class net.sf.basedb.core.ExtraValue

Creates a new extra value item from the given data.

EXTRAVALUE - Enum constant in enum class net.sf.basedb.core.Item

The item is an ExtraValue

EXTRAVALUE_DATA - Static variable in class net.sf.basedb.core.File

The id for the FileType item representing a file containing analysed extra value data.

ExtraValue.CoordinateType - Enum Class in net.sf.basedb.core

Defines which coordinates in the data cube the extra values are attached to.

extraValueColumns - Static variable in class net.sf.basedb.core.VirtualColumn

A cache of virtual column objects for extra value types.

ExtraValueData - Class in net.sf.basedb.core.data

This represents the use of extra values that have been calculated for a bioassayset.

ExtraValueData() - Constructor for class net.sf.basedb.core.data.ExtraValueData

ExtraValueExpression - Class in net.sf.basedb.core

Represents the value of an extra value in a dynamic query: alias.value.

ExtraValueExpression(ExtraValue) - Constructor for class net.sf.basedb.core.ExtraValueExpression

Create a new expression for the specified extra value.

ExtraValueFunction - Class in net.sf.basedb.util.jep

A JEP function class that adds a xtra(int) function to a JEP expression parser.

ExtraValueFunction(DbControl, Map<Integer, Integer>) - Constructor for class net.sf.basedb.util.jep.ExtraValueFunction

Create a new instance of this function which can be used to dynamically evaluate expressions.

ExtraValueFunction(DbControl, BioAssaySet) - Constructor for class net.sf.basedb.util.jep.ExtraValueFunction

Create a new instance of this function.

ExtraValueJoin - Class in net.sf.basedb.core

Represents a join to an extra value in a dynamic query: leftTable JOIN extraValueTable ON ...

ExtraValueJoin(ExtraValue, JoinType) - Constructor for class net.sf.basedb.core.ExtraValueJoin

Create a new join using the root entity table as the left table.

ExtraValueJoiner(JoinType) - Constructor for class net.sf.basedb.core.DynamicPositionQueryJoiners.ExtraValueJoiner

ExtraValueJoiner(JoinType) - Constructor for class net.sf.basedb.core.DynamicSpotQueryJoiners.ExtraValueJoiner

extraValues - Variable in class net.sf.basedb.core.data.BioAssaySetData

extraValues - Variable in class net.sf.basedb.core.data.DataCubeData

extraValues - Variable in class net.sf.basedb.core.data.ExtraValueTypeData

extraValueType - Variable in class net.sf.basedb.core.data.ExtraValueData

ExtraValueType - Class in net.sf.basedb.core

Defines extra values that can be calculated by plugins or some other application and inserted as part of a BioAssaySet.

ExtraValueType(ExtraValueTypeData) - Constructor for class net.sf.basedb.core.ExtraValueType

Creates a new extra value type item.

EXTRAVALUETYPE - Enum constant in enum class net.sf.basedb.core.Item

The item is an ExtraValueType

ExtraValueTypeData - Class in net.sf.basedb.core.data

This represents the definitiona of an extra value type that can be calculated by a plugin.

ExtraValueTypeData() - Constructor for class net.sf.basedb.core.data.ExtraValueTypeData

extraValueTypeParameter - Variable in class net.sf.basedb.plugins.JepExtraValueCalculator

F

factor - Variable in class net.sf.basedb.util.units.LinearUnitConverter

factorQuery - Variable in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter

factory - Variable in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory.MySkinAction

factory - Variable in class net.sf.basedb.core.log.db.AnnotationLogger

factory - Variable in class net.sf.basedb.core.log.db.AnnotationSetLogger

factory - Variable in class net.sf.basedb.core.log.db.AnyToAnyLogger

factory - Variable in class net.sf.basedb.core.log.db.BioMaterialEventLogger

factory - Variable in class net.sf.basedb.core.log.db.DefaultEntityLogger

factory - Variable in class net.sf.basedb.core.log.db.FileSetMemberLogger

factory - Variable in class net.sf.basedb.core.log.db.ManualEntryLogger

factory - Variable in class net.sf.basedb.core.log.db.PlateEventLogger

factory - Variable in class net.sf.basedb.core.log.LoggingInterceptor.LogManagerAndFactory

factory - Variable in class net.sf.basedb.util.extensions.manager.FactoryParametersKey

factory - Variable in class net.sf.basedb.util.listable.SourceItemTransformerWithCache

factory - Variable in class net.sf.basedb.util.uri.http.HttpConnectionManagerActionFactory

factoryId - Variable in class net.sf.basedb.util.uri.ConnectionParameters

factoryKey - Variable in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader

factoryParameters - Variable in class net.sf.basedb.util.extensions.xml.XmlLoader

FactoryParametersKey - Class in net.sf.basedb.util.extensions.manager

Key implementation used for configuration parameters for factories.

FactoryParametersKey(Object) - Constructor for class net.sf.basedb.util.extensions.manager.FactoryParametersKey

Create a new key for the given factory.

failIfItemExists - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

failIfMultipleFoundItems - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

failIfMultipleFoundItems - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

failIfMultipleFoundReferences - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

failIfMultipleFoundTargets - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

failIfMultiplePositions - Variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter

failIfMultipleSourceItems - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

failIfNotFoundItems - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

failIfNotFoundReference - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

failIfNotFoundSource - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

failIfNotFoundTarget - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

failIfNoUsePermissionToReference - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

failIfNoUsePermissionToTarget - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

failIfNoWritePermissionToItem - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

failIfNoWritePermissionToSource - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

failIfTooManyValues - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

failIfUsed - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

failSafe - Variable in class net.sf.basedb.core.AbstractQuery

If transactions must be able to continue after an SQL failure or not.

Failure - Class in net.sf.basedb.util.overview

Holds information about a failed validation.

Failure(ValidationRuleAction, Node) - Constructor for class net.sf.basedb.util.overview.Failure

Create a new validation failure.

Failure(ValidationRuleAction, Node, String) - Constructor for class net.sf.basedb.util.overview.Failure

Create a new validation failure with a detailed message.

Failure(ValidationRuleAction, Node, String, Fix...) - Constructor for class net.sf.basedb.util.overview.Failure

Create a new validation failure with a detailed message and a list of suggested fixes.

failures - Variable in class net.sf.basedb.util.overview.GenericOverview

failureSummary - Variable in class net.sf.basedb.util.overview.Validator

FallbackIdMethod - Class in net.sf.basedb.plugins.batchimport

Identification method implementation that first tries a parent id method, and, if no item is found and the identifier is a number, tries to load the item by id.

FallbackIdMethod(String, String, IdMethod) - Constructor for class net.sf.basedb.plugins.batchimport.FallbackIdMethod

Create a new id method.

FALSE - Static variable in class net.sf.basedb.core.migrate.BooleanWriter

FALSE - Static variable in class net.sf.basedb.util.excel.ExcelValue

falseValue - Variable in enum class net.sf.basedb.util.formatter.BooleanFormatter.Type

FastAnnotation(Object[]) - Constructor for class net.sf.basedb.core.FastAnnotationLoader.FastAnnotation

FastAnnotationLoader<T> - Class in net.sf.basedb.core

Implements an API for simple and fast loading of annotation values optimized for situations when a single annotation is needed for many (=thousands) of items.

FastAnnotationLoader(DbControl, AnnotationType) - Constructor for class net.sf.basedb.core.FastAnnotationLoader

FastAnnotationLoader.FastAnnotation<T> - Class in net.sf.basedb.core

Holds information about a single annotation value.

FastAnnotationLoader.FastIterator<T> - Class in net.sf.basedb.core

Iterator implementation that splits the query into multiple calls depending on the max number of parameters that can be used in a query.

FastIterator(DbControl, AnnotationType, Item, int, boolean, List<Integer>) - Constructor for class net.sf.basedb.core.FastAnnotationLoader.FastIterator

FastLinkLoader(DbControl, Item, String, Item) - Constructor for class net.sf.basedb.core.AnyToAny.FastLinkLoader

FATAL - Enum constant in enum class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory.Level

fatalError(SAXParseException) - Method in class net.sf.basedb.util.XmlUtil2.Validator

Fatal errors thrown with a detailed error message.

favicon - Variable in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory

favicon - Variable in class net.sf.basedb.clients.web.taglib.Page

The 'favicon' to use.

fax - Variable in class net.sf.basedb.core.authentication.ExtraUserInformation

fax - Variable in class net.sf.basedb.core.data.UserData

feature - Variable in class net.sf.basedb.core.data.RawData

Feature - Class in net.sf.basedb.core

This is a utility class for Features.

Feature() - Constructor for class net.sf.basedb.core.Feature

FEATURE - Enum constant in enum class net.sf.basedb.core.Item

The item is a Feature.

FEATURE_EXTRACTION - Static variable in class net.sf.basedb.core.Protocol

The ID for the feature extraction protocol type, for example a protocol used for analysing one or more images to create a raw data file.

FEATURE_EXTRACTION - Static variable in class net.sf.basedb.core.Software

The id for the SoftwareType item representing the softwaretype "feature extraction software".

FEATURE_ID - Enum constant in enum class net.sf.basedb.core.FeatureIdentificationMethod

Use the external feature ID.

featureBatcher - Variable in class net.sf.basedb.core.ArrayDesign

FeatureBatcher - Class in net.sf.basedb.core

Batcher class for Features or AffyFeatures.

FeatureBatcher(DbControl, ArrayDesign) - Constructor for class net.sf.basedb.core.FeatureBatcher

FeatureCoordinate - Class in net.sf.basedb.core

Represents the coordinate of a feature on an array design.

FeatureCoordinate(Integer, Integer, Integer, Integer, Integer) - Constructor for class net.sf.basedb.core.FeatureCoordinate

Create new object with the specified row and column.

FeatureData - Class in net.sf.basedb.core.data

This class holds information about a regular feature.

FeatureData() - Constructor for class net.sf.basedb.core.data.FeatureData

FeatureData(ArrayDesignBlockData, ReporterData) - Constructor for class net.sf.basedb.core.data.FeatureData

Create a new feature which is linked to a reporter only.

FeatureData(ArrayDesignBlockData, WellData) - Constructor for class net.sf.basedb.core.data.FeatureData

Create a new feature which is linked to a well.

featureDiameter - Variable in class net.sf.basedb.core.data.ArrayDesignBlockData

featureId - Variable in class net.sf.basedb.core.RawDataBatcher.FeatureInfo

featureIdColumnMapping - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

featureIdColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

featureIdentificationMethod - Variable in class net.sf.basedb.core.data.ArrayDesignData

FeatureIdentificationMethod - Enum Class in net.sf.basedb.core

This enumeration defines constants that are used to specify which method to use for identifying features on an array design.

FeatureIdentificationMethod(int, boolean, String) - Constructor for enum class net.sf.basedb.core.FeatureIdentificationMethod

Creates a new feature identification method.

featureIdentificationParameter - Static variable in class net.sf.basedb.plugins.IlluminaRawDataImporter

featureIdentificationParameter - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

featureIdMapper - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

featureIdMapper - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

featureIds - Variable in class net.sf.basedb.core.FeatureBatcher

Holds identification of already inserted features.

FeatureInfo(FeatureData) - Constructor for class net.sf.basedb.core.RawDataBatcher.FeatureInfo

featureMismatchErrorParameter - Static variable in class net.sf.basedb.plugins.IlluminaRawDataImporter

featureMismatchErrorParameter - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

featureProxy - Variable in class net.sf.basedb.core.RawDataBatcher

FeatureProxy() - Constructor for class net.sf.basedb.core.RawDataBatcher.FeatureProxy

features - Variable in class net.sf.basedb.core.data.ArrayDesignBlockData

fetch - Variable in class net.sf.basedb.core.query.HqlInnerJoin

fetch - Variable in class net.sf.basedb.core.query.HqlLeftJoin

fetchSize - Variable in class net.sf.basedb.core.Migration

ffp - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

ffp - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

ffp - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

ffp - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter

ffp - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter

ffp - Variable in class net.sf.basedb.plugins.PlateMappingImporter

ffp - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

ffp - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

ffp - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

ffp - Variable in class net.sf.basedb.util.bfs.AnnotationParser

ffp - Variable in class net.sf.basedb.util.bfs.DataParser

ffp - Variable in class net.sf.basedb.util.bfs.MetadataParser

FieldInfo - Class in net.sf.basedb.clients.web.extensions.login

Information about a the login/password fields on the login form.

FieldInfo() - Constructor for class net.sf.basedb.clients.web.extensions.login.FieldInfo

FieldInfo(String, boolean) - Constructor for class net.sf.basedb.clients.web.extensions.login.FieldInfo

file - Variable in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext

file - Variable in class net.sf.basedb.core.data.FileSetMemberData

file - Variable in class net.sf.basedb.core.data.ProtocolData

file - Variable in class net.sf.basedb.core.File.UploadStream

The file to write to.

file - Variable in class net.sf.basedb.util.AutoDetectFileFormat.IsImportableFilter

file - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile

file - Variable in class net.sf.basedb.util.extensions.manager.Settings

file - Variable in class net.sf.basedb.util.FileExportOutputStream

file - Variable in class net.sf.basedb.util.FileImportInputStream

file - Variable in class net.sf.basedb.util.importer.BaseFileWrapper

file - Variable in class net.sf.basedb.util.importer.DiskFileWrapper

file - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo

file() - Static method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext

Creates a file-listing or single-file context without any other related items.

File - Class in net.sf.basedb.core

This class is used to represent individual file items and information about them.

File(FileData) - Constructor for class net.sf.basedb.core.File

Creates a new file item from the given data.

FILE - Enum constant in enum class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext.Type

The context is a regular file listing context.

FILE - Enum constant in enum class net.sf.basedb.core.Item

The item is a File.

FILE - Enum constant in enum class net.sf.basedb.core.Path.Type

The path is a path to a File.

FILE - Static variable in class net.sf.basedb.core.QuotaType

The ID for the file.

FILE_INFORMATION - Enum constant in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section

FILE_VERSION - Static variable in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot

The version number for the file format in use when serializing this data.

File.CharsetTesterThread - Class in net.sf.basedb.core

File.UploadStream - Class in net.sf.basedb.core

This class is used for uploading a file.

fileActions - Variable in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerUtil

FileAttachable - Interface in net.sf.basedb.core

A FileAttachable item is an item that can have a File attached to it.

FileAttachableData - Interface in net.sf.basedb.core.data

A fileattachable item is an item which can have a File attached to it.

fileCache - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

fileColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter

fileColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

fileColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

fileContext - Variable in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerUtil

FileCopyRunnable - Class in net.sf.basedb.util

Runnable implementation that copies data from an input stream to an output stream when executed.

FileCopyRunnable(InputStream, OutputStream) - Constructor for class net.sf.basedb.util.FileCopyRunnable

Create a new file copy object.

FileData - Class in net.sf.basedb.core.data

This class holds information about a file.

FileData() - Constructor for class net.sf.basedb.core.data.FileData

FileData() - Constructor for class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor.FileData

FileExportOutputStream - Class in net.sf.basedb.util

An extension to the ExportOutputStream class which directs the output to a File in BASE.

FileExportOutputStream(File, boolean) - Constructor for class net.sf.basedb.util.FileExportOutputStream

Create a new export stream that writes the exported data to a file in the BASE filesystem

fileFeatures - Variable in class net.sf.basedb.core.data.ArrayDesignData

fileFromKey(String) - Method in class net.sf.basedb.util.StaticCache

fileGui - Static variable in class net.sf.basedb.plugins.PackedFileExporter

fileId - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay

FileImporter - Class in net.sf.basedb.plugins.batchimport

Plug-in for importing file items in a batch.

FileImporter() - Constructor for class net.sf.basedb.plugins.batchimport.FileImporter

FileImporter.PathIdMethod - Class in net.sf.basedb.plugins.batchimport

FileImportInputStream - Class in net.sf.basedb.util

An extension to the ImportInputStream class which reads from a file on the BASE file system.

FileImportInputStream(File, long, String) - Constructor for class net.sf.basedb.util.FileImportInputStream

Create a new import stream that reads data from a file in the BASE filesystem.

fileIterator - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

FileIterator(List<RawBioAssay>, List<File>) - Constructor for class net.sf.basedb.plugins.RawDataFlatFileImporter.FileIterator

FileLoader - Class in net.sf.basedb.util.overview.loader

Node loader implementation for files.

FileLoader() - Constructor for class net.sf.basedb.util.overview.loader.FileLoader

fileMapper - Variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter

fileMapper - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

fileMapper - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

filename - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload.SectionHeaders

filename - Variable in class net.sf.basedb.clients.web.fileupload.UploadedFile

filename - Variable in class net.sf.basedb.core.Path

The filename part of the path.

filename - Variable in class net.sf.basedb.plugins.HelpImporter

filename - Variable in class net.sf.basedb.util.bfs.AnnotationParser

filename - Variable in class net.sf.basedb.util.bfs.AnnotationWriter

filename - Variable in class net.sf.basedb.util.bfs.DataParser

filename - Variable in class net.sf.basedb.util.bfs.DataWriter

filename - Variable in class net.sf.basedb.util.bfs.MetadataParser

filename - Variable in class net.sf.basedb.util.bfs.MetadataWriter

FILENAME_PATTERN - Static variable in class net.sf.basedb.clients.web.fileupload.FileUpload

filenameGenerator - Variable in class net.sf.basedb.util.bfs.AbstractDataWriterFactory

FilenameGenerator<T> - Interface in net.sf.basedb.util.bfs

File name generators are used together with DataWriterFactory implementations to generate file names for BFS data files.

fileOnly - Variable in class net.sf.basedb.core.data.PlatformData

fileOnly - Variable in class net.sf.basedb.core.data.PlatformVariantData

fileOnly - Variable in class net.sf.basedb.core.RawDataType

FileOnlyImporterSupport - Class in net.sf.basedb.plugins.executor

Importer implementation for the external program executor that uploads all created files to BASE and attaches them to a child bioassay set.

FileOnlyImporterSupport() - Constructor for class net.sf.basedb.plugins.executor.FileOnlyImporterSupport

FilePacker - Interface in net.sf.basedb.util.zip

This interface should be implemented by classes that can pack files and directories from BASE file system.

fileParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter

Parameter definition that asks for the file that should be imported.

fileParameter - Static variable in class net.sf.basedb.plugins.Base1PluginExecuter

Parameter definition that asks for the configuration file that should be imported.

fileParameter - Variable in class net.sf.basedb.plugins.HelpImporter

FileParameterType - Class in net.sf.basedb.core

This class represent a parameter type that is a file.

FileParameterType() - Constructor for class net.sf.basedb.core.FileParameterType

Create a new file parameter type, allowing null values.

FileParameterType(File, boolean, int) - Constructor for class net.sf.basedb.core.FileParameterType

Create a new file parameter type.

FilePathFormatter - Class in net.sf.basedb.util.formatter

Formatter implementation that format File items to their complete paths.

FilePathFormatter() - Constructor for class net.sf.basedb.util.formatter.FilePathFormatter

Create a new formatter.

FilePathFormatter(String) - Constructor for class net.sf.basedb.util.formatter.FilePathFormatter

Create a new formatter.

filePattern - Variable in class net.sf.basedb.util.RegexpFileFilter

fileResults - Variable in class net.sf.basedb.util.extensions.manager.ProcessResults

FileResults(ExtensionsFile, ProcessResults.FileResults) - Constructor for class net.sf.basedb.util.extensions.manager.ProcessResults.FileResults

files - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload

Contains information about uploaded files name --> UploadedFile

files - Variable in class net.sf.basedb.core.data.DirectoryData

files - Variable in class net.sf.basedb.core.data.FileServerData

files - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter.FileIterator

files - Variable in class net.sf.basedb.util.bfs.MetadataModel

fileServer - Variable in class net.sf.basedb.core.data.FileData

FileServer - Class in net.sf.basedb.core

This class represents a file server that is used to store external files.

FileServer(FileServerData) - Constructor for class net.sf.basedb.core.FileServer

FILESERVER - Enum constant in enum class net.sf.basedb.core.Item

The item is a FileServer.

fileServerColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.FileImporter

FileServerData - Class in net.sf.basedb.core.data

File entries that are external files can be linked to a file server.

FileServerData() - Constructor for class net.sf.basedb.core.data.FileServerData

fileServerMapper - Variable in class net.sf.basedb.plugins.batchimport.FileImporter

fileServerQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

fileSet - Variable in class net.sf.basedb.core.data.ArrayDesignData

fileSet - Variable in class net.sf.basedb.core.data.BioAssaySetData

fileSet - Variable in class net.sf.basedb.core.data.DerivedBioAssayData

fileSet - Variable in class net.sf.basedb.core.data.ExtraValueData

fileSet - Variable in class net.sf.basedb.core.data.FileSetMemberData

fileSet - Variable in class net.sf.basedb.core.data.RawBioAssayData

FileSet - Class in net.sf.basedb.core

A file set is the container for files that have been attach to an item to hold data instead of importing it to the database.

FileSet(FileSetData) - Constructor for class net.sf.basedb.core.FileSet

Regular constructor if the item is not known beforehand.

FileSet(FileSetData, FileStoreEnabled) - Constructor for class net.sf.basedb.core.FileSet

Special constructor to avoid FileSet.getItem() to hit the database when the item is known beforehand.

FILESET - Enum constant in enum class net.sf.basedb.core.Item

The item is a FileSet

FileSet.QueryRuntimeFilterImpl - Class in net.sf.basedb.core

FileSetData - Class in net.sf.basedb.core.data

This class collects all files used to store data for an item that store data in files instead of in the database.

FileSetData() - Constructor for class net.sf.basedb.core.data.FileSetData

fileSetId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba

FileSetMember - Class in net.sf.basedb.core

This class represents a file that is member of a file set.

FileSetMember(FileSetMemberData) - Constructor for class net.sf.basedb.core.FileSetMember

Creates a new member item from the given data.

FILESETMEMBER - Enum constant in enum class net.sf.basedb.core.Item

The item is a FileSetMember

FileSetMember.QueryRuntimeFilterImpl - Class in net.sf.basedb.core

FileSetMemberData - Class in net.sf.basedb.core.data

This class hols information about individual files attached to items that store data in files instead of in the database.

FileSetMemberData() - Constructor for class net.sf.basedb.core.data.FileSetMemberData

FileSetMemberLoader - Class in net.sf.basedb.clients.web.plugins

Data loader implementation that load the files in a file set in FileStoreEnabled items.

FileSetMemberLoader() - Constructor for class net.sf.basedb.clients.web.plugins.FileSetMemberLoader

FileSetMemberLoader(DataFileType, Metadata.PropertyPath<FileSetMember, ?>) - Constructor for class net.sf.basedb.clients.web.plugins.FileSetMemberLoader

Load only members of the given file type and then use the given property path to load a specific property of the member.

FileSetMemberLogger - Class in net.sf.basedb.core.log.db

Logger for file set members that logs changes as updates to the parent item the file belong to.

FileSetMemberLogger(DbLogManagerFactory) - Constructor for class net.sf.basedb.core.log.db.FileSetMemberLogger

FileSetMemberNameGenerator - Class in net.sf.basedb.util.overview.node

Since a FileSetMember isn't Nameable we construct the name by combining the name of the file type and the name of the file.

FileSetMemberNameGenerator() - Constructor for class net.sf.basedb.util.overview.node.FileSetMemberNameGenerator

fileSize - Variable in class net.sf.basedb.util.bfs.AnnotationParser

fileSize - Variable in class net.sf.basedb.util.bfs.DataParser

fileSize - Variable in class net.sf.basedb.util.bfs.MetadataParser

fileSpots - Variable in class net.sf.basedb.core.data.RawBioAssayData

fileSpotsMapper - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

fileSpotsMapping - Static variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

filesToIgnore - Variable in class net.sf.basedb.util.extensions.manager.processor.IgnoreFileProcessor

FileStoreEnabled - Interface in net.sf.basedb.core

This interface is implemented by items that can use files instead of the database for storing data.

FileStoreEnabledData - Interface in net.sf.basedb.core.data

Items implementing this interface can store data in files instead of in the database.

fileStoreEnabledItems - Static variable in class net.sf.basedb.core.Metadata

FileStoreUtil - Class in net.sf.basedb.core

Utility class working with FileStoreEnabled items.

FileStoreUtil() - Constructor for class net.sf.basedb.core.FileStoreUtil

fileType - Variable in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext

fileType - Variable in class net.sf.basedb.clients.web.formatter.DataFileFormatter

fileType - Variable in class net.sf.basedb.clients.web.plugins.FileSetMemberLoader

fileType - Variable in class net.sf.basedb.core.data.FileSetMemberData

fileType - Variable in class net.sf.basedb.core.data.FileTypeIndex

fileType - Variable in class net.sf.basedb.core.data.ItemSubtypeFileTypeData

fileType - Variable in class net.sf.basedb.core.data.MimeTypeData

fileType - Variable in class net.sf.basedb.core.data.PlatformFileTypeData

fileType - Variable in class net.sf.basedb.core.Install.PlatformFT

fileType - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter

fileType - Variable in class net.sf.basedb.util.overview.Fix

fileTypeColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter

fileTypeColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

fileTypeColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

fileTypeId - Variable in class net.sf.basedb.util.fileset.SingleFileValidationAction

FileTypeIndex - Class in net.sf.basedb.core.data

This is a helper class for the PlatformData item to help with the Hibernate mapping to PlatformFileTypeData object.

FileTypeIndex() - Constructor for class net.sf.basedb.core.data.FileTypeIndex

FileTypeIndex(PlatformVariantData, DataFileTypeData) - Constructor for class net.sf.basedb.core.data.FileTypeIndex

fileTypeMapper - Variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter

fileTypeMapper - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

fileTypeMapper - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

fileTypeQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

fileTypes - Variable in class net.sf.basedb.core.data.ItemSubtypeData

fileTypes - Variable in class net.sf.basedb.core.data.PlatformData

fileTypes - Variable in class net.sf.basedb.core.data.PlatformVariantData

fileTypes - Variable in class net.sf.basedb.core.MigrateRbaToDba.LineMapping

fileTypes - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba

FileUnpacker - Interface in net.sf.basedb.util.zip

This interface should be implemented by plugins that can unpack a single compressed file into the BASE file system.

FileUpload - Class in net.sf.basedb.clients.web.fileupload

Objects of this class are used to handle file upload from browsers using the standard mechanism described in RFC1867.

FileUpload(ServletRequest) - Constructor for class net.sf.basedb.clients.web.fileupload.FileUpload

Create a new FileUpload object which will read the posted data from the given ServletRequest object.

FileUpload(ServletRequest, int, long) - Constructor for class net.sf.basedb.clients.web.fileupload.FileUpload

Create a new FileUpload object which will read the posted data from the given ServletRequest object limiting the transfer rate.

FileUpload.SectionHeaders - Class in net.sf.basedb.clients.web.fileupload

This class contains information extracted from the section headers for a form field or file upload field.

FileUpload.UploadStatus - Class in net.sf.basedb.clients.web.fileupload

This class contains information about the read status on the ServletInputStream

FileUpload.UploadStream - Class in net.sf.basedb.clients.web.fileupload

FileUploadProgress - Class in net.sf.basedb.clients.web.fileupload

Objects of this class holds information about the progress of an upload.

FileUploadProgress(long) - Constructor for class net.sf.basedb.clients.web.fileupload.FileUploadProgress

Create a new FileUploadProgress object.

FileUtil - Class in net.sf.basedb.util

This class collects some useful methods for file and stream handling.

FileUtil() - Constructor for class net.sf.basedb.util.FileUtil

FileValidator - Class in net.sf.basedb.util.overview.validator

Validator implementation for files.

FileValidator() - Constructor for class net.sf.basedb.util.overview.validator.FileValidator

fileViewer - Variable in class net.sf.basedb.clients.web.extensions.list.AnyLinkColumn

fileViewer - Variable in class net.sf.basedb.clients.web.formatter.AutoLinkFormatter

fileViewer - Variable in class net.sf.basedb.clients.web.formatter.DataFileFormatter

fileViewer - Variable in class net.sf.basedb.clients.web.formatter.LinkedFileFormatter

FileViewerContext - Class in net.sf.basedb.clients.web.extensions.fileviewer

This class is used for holding information about a file that is beeing displayed in the GUI in some context.

FileViewerContext(FileViewerContext.Type, BasicItem) - Constructor for class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext

FileViewerContext.Type - Enum Class in net.sf.basedb.clients.web.extensions.fileviewer

FileViewerUtil - Class in net.sf.basedb.clients.web.extensions.fileviewer

Helper class for handling the "file-viewer" extension point.

FileViewerUtil(JspContext, FileViewerContext) - Constructor for class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerUtil

Deprecated.

In 3.17, use FileViewerUtil.getOrCreate(JspContext, FileViewerContext) instead

FileWrapper - Interface in net.sf.basedb.util.importer

Wrapper around files that provide some basic information about the file.

fillText - Variable in class net.sf.basedb.clients.web.taglib.menu.Menu

Optional text to display to the far right of a horizontal menu

filter - Variable in class net.sf.basedb.core.query.ConditionalQueryElement

filter - Variable in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor

filter - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredEventHandler

filter - Variable in class net.sf.basedb.util.extensions.xml.XmlLoader

filter - Variable in class net.sf.basedb.util.IncludeExcludeFilter

filter - Variable in class net.sf.basedb.util.StaticCache.CleanupTask

filter(Collection<? extends T>, Filter<? super T>) - Static method in class net.sf.basedb.util.filter.FilterUtil

Filter a collection and return a new collection with the objects that passes the Filter.evaluate(Object) method.

Filter<T> - Interface in net.sf.basedb.util.filter

A filter is something that selectes or rejects an object due to some property of it.

FILTER - Enum constant in enum class net.sf.basedb.core.VirtualTable

Table that holds column/position coordinates that remains after a filtering operation has been applied to a data cube layer.

FILTER - Static variable in class net.sf.basedb.core.VirtualColumn

This column stores the data cube filter number.

filterable - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

filterable - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

filterable - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef

If the column is filterable or not

filterable - Variable in class net.sf.basedb.clients.web.taglib.table.TableColumn

filterAnnotationType - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

filterAnnotationTypeName - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

filterAnnotationValue - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

filterBatcher - Variable in class net.sf.basedb.core.BioAssaySet

The one and only filter batcher for this bioassayset.

FilterBatcher - Class in net.sf.basedb.core

Batcher class for filtered bioassaysets.

FilterBatcher(DbControl, BioAssaySet) - Constructor for class net.sf.basedb.core.FilterBatcher

Create a new filter batcher for a bioassayset.

filterChain - Variable in class net.sf.basedb.core.QueryRuntimeFilterFactory.ChainedFilter

The list of chained filters.

filterClass - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

filterClass - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef

Extra CSS class to add to the filter table cell.

FilterConfigurator() - Constructor for class net.sf.basedb.core.HibernateUtil.FilterConfigurator

filterGroup - Variable in class net.sf.basedb.core.data.ItemListSyncFilterData

filterItemList - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

filterItemListName - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

filterManager - Variable in class net.sf.basedb.core.AbstractEntityQuery

The manager of the runtime query filters.

filterNo - Variable in class net.sf.basedb.core.data.DataCubeFilterData

filterOnSelectedItems(EntityQuery) - Method in class net.sf.basedb.core.ItemContext

Add a filter to the given query that restricts it to only return items that have been selected.

filterProperty - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

filterProperty - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

filterProperty - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef

Optional property used for filtering.

filters - Variable in class net.sf.basedb.core.data.DataCubeData

filters - Variable in class net.sf.basedb.core.SyncFilter

filters - Variable in class net.sf.basedb.util.extensions.events.CombiningEventFilter

filterSql - Variable in class net.sf.basedb.core.FilterBatcher

The statement that inserts filter data.

filterSqlStatement - Variable in class net.sf.basedb.core.FilterBatcher

The SQL string for the FilterBatcher.filterSql statement.

filterTemplates - Variable in class net.sf.basedb.core.HibernateUtil.FilterConfigurator

filterText - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

filterText - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef

Text to display in the filter cell when the column is not filterable.

FilterUtil - Class in net.sf.basedb.util.filter

Utility class for working with and using filters.

FilterUtil() - Constructor for class net.sf.basedb.util.filter.FilterUtil

fiMethod - Variable in class net.sf.basedb.core.FeatureBatcher

fiMethod - Variable in class net.sf.basedb.core.RawDataBatcher

The method to use for identifying features.

fiMethod - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter

finalizeRegistration(ExtensionsManager) - Method in class net.sf.basedb.util.extensions.manager.processor.IgnoreFileProcessor

Finalize the ignore registration.

finalizeRegistration(ExtensionsManager, boolean) - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor

find(Class<T>, Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

find(Class<T>, Object, Map<String, Object>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

find(Class<T>, Object, LockModeType) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

find(Class<T>, Object, LockModeType, Map<String, Object>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

find(Set<QuotaIndex>) - Method in class net.sf.basedb.core.data.QuotaIndex

Find the quota entry in the given set that correpsonds to the same quota type and location as this index.

find(DbControl, ItemQuery<I>, String) - Method in class net.sf.basedb.plugins.batchimport.AnnotationIdMethod

Find all items with property = identifier.

find(DbControl, ItemQuery<I>, String) - Method in class net.sf.basedb.plugins.batchimport.FallbackIdMethod

First, find items using the parent id method.

find(DbControl, ItemQuery<I>, String) - Method in class net.sf.basedb.plugins.batchimport.FileImporter.PathIdMethod

find(DbControl, ItemQuery<I>, String) - Method in interface net.sf.basedb.plugins.batchimport.IdMethod

Try to find items with this query method.

find(DbControl, ItemQuery<I>, String) - Method in class net.sf.basedb.plugins.batchimport.InternalIdMethod

Find the item with id = identifier

find(DbControl, ItemQuery<I>, String) - Method in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod

Find all items with property[0] = identifier, or property[1] = identifier, ....

find(DbControl, ItemQuery<I>, String) - Method in class net.sf.basedb.plugins.batchimport.PropertyIdMethod

Find all items with property = identifier.

find(AnnotationSetSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil

Same as findAll but only return a boolean instead of the number of snapshots found.

find(AnnotationSetSnapshot, Filter<AnnotationSnapshot>) - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil

Same as findAll but only return a boolean instead of the number of snapshots found.

FIND_WHAT - Static variable in exception net.sf.basedb.core.ItemModifiedException

A pattern to extract the Xxxx and id parts from a string containing [net.sf.basedb.core.data.XxxxData#id].

findAll(Set<String>) - Method in class net.sf.basedb.core.dbengine.TableInfo

Find all indexes with the given set of columns.

findAll(AnnotationSetSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil

Find and load annotations from the given annotation set snapshot.

findAll(AnnotationSetSnapshot, Filter<AnnotationSnapshot>) - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil

Find and load annotations from the given annotation set snapshot using an optional extra filter.

findAll(Filter<? super Node>) - Method in class net.sf.basedb.util.overview.Node

Find all nodes in the parent chain that matches the given filter.

findAllDefaultData(Item, ItemSubtypeData, boolean) - Method in class net.sf.basedb.core.Project

Find all default items in this project of the given item type (required) and subtype (optional).

findAnnotations(DbControl, Annotatable, Filter<? super AnnotationSnapshot>, boolean) - Method in class net.sf.basedb.core.snapshot.SnapshotManager

findAnnotations(DbControl, Annotatable, Filter<? super AnnotationSnapshot>, boolean, boolean) - Method in class net.sf.basedb.core.snapshot.SnapshotManager

Utility method for calling getSnapshot and findAnnotations in one go.

findAnnotations(DbControl, AnnotationSetSnapshot, Filter<? super AnnotationSnapshot>, boolean) - Method in class net.sf.basedb.core.snapshot.SnapshotManager

Find annotations.

findAnnotations(DbControl, AnnotationSetSnapshot, Filter<? super AnnotationSnapshot>, boolean, boolean) - Method in class net.sf.basedb.core.snapshot.SnapshotManager

Search in a snapshot for all annotations matching a given filter.

findAnnotationTypeCategory(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Find an annotation type category with a given identifier.

findArrayBatch(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Find an array batch with a given identifier.

findArrayDesign(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Find an array design with a given identifier.

findArraySlide(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Find an array slide with a given identifier.

findBioAssay(List<DerivedBioAssay>, String) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter

findBioPlate(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Find a bioplate with a given identifier.

findBioPlateType(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Find a bioplate type with a given identifier.

findBioSource(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Same as AbstractItemImporter.findBioSource(DbControl, IdMethod, String, ItemSubtype) with a null item subtype.

findBioSource(DbControl, IdMethod, String, ItemSubtype) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Find a biosource with a given identifier.

findBioWell(DbControl, BioPlate, String, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Find a well on a bioplate.

findChildren - Variable in class net.sf.basedb.core.BioAssaySet

Query to retrieve children for a bioassayset.

findClass(String) - Method in class net.sf.basedb.util.JarClassLoader

findClass(String) - Method in class net.sf.basedb.util.JarClassLoader.JarClassLoaderProxy

findColumn - Static variable in class net.sf.basedb.util.parser.FlatFileParser

Pattern used to find column mappings in a string, ie. abc \col\ def

findColumn(String) - Method in class net.sf.basedb.core.dbengine.TableInfo

Find information about a column with the given name.

findColumn(String) - Method in class net.sf.basedb.util.parser.ColFunction

Find column index by checking each column header against a regular expression.

findColumnHeaderIndex(String) - Method in class net.sf.basedb.util.parser.FlatFileParser

Find the index of a column header using a regular expression for pattern matching.

findConstructor(Class<I>, Object[]) - Static method in class net.sf.basedb.util.ClassUtil

Find a constructor for the specified class which takes parameters of the specified types taking superclasses and interfaces into account.

findDataFileType(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Find a data file type with a given identifier.

findDefaultData(DbControl, String, boolean) - Method in class net.sf.basedb.core.Project

findDefaultData(Item, ItemSubtypeData, boolean) - Method in class net.sf.basedb.core.Project

Find a default item in this project of the given item type (required) and subtype (optional).

findDefaultItem() - Method in class net.sf.basedb.util.parser.DefaultItemFunction

Find a default item.

findDefaultItems(DbControl, Item, boolean) - Method in class net.sf.basedb.core.Project

Find the default items of the given item type.

findDefaultItems(DbControl, ItemSubtype, boolean) - Method in class net.sf.basedb.core.Project

Find the default (subtypable) items that has the given subtype.

findDefaultItemsOfRelatedSubtype(DbControl, ItemSubtype, Item) - Method in class net.sf.basedb.core.Project

Utility method for finding default items of the given relatedType.

findDefaultRelatedData(DbControl, Subtypable, Item, boolean) - Method in class net.sf.basedb.core.Project

findDerivedBioAssay(DbControl, IdMethod, String, ItemSubtype) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Find a derived bioassay with a given identifier.

findExtract(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Same as AbstractItemImporter.findSample(DbControl, IdMethod, String, ItemSubtype) with a null subtype.

findExtract(DbControl, IdMethod, String, ItemSubtype) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Find an extract with a given identifier.

findFactory(URI) - Static method in class net.sf.basedb.util.uri.ConnectionManagerUtil

Find a factory for the given URI.

findFiles(File, FileFilter) - Static method in class net.sf.basedb.util.FileUtil

Find files matching a given filter in a directory.

findFileServer(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Find a file server with a given identifier.

findFirstCommon(Collection<T>, Collection<T>, T) - Static method in class net.sf.basedb.util.ListUtil

Find the first entry in the master collection that is also present in the check collection.

findForeignKeyName(String, Set<String>, String) - Method in class net.sf.basedb.core.dbengine.TableInfo

Check if there is a foreign key with the same name or exactly the same set of columns referencing the same table.

findGeometry(DbControl, int, int) - Method in class net.sf.basedb.plugins.PlateMappingImporter

findHardware(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Same as AbstractItemImporter.findHardware(DbControl, IdMethod, String, ItemSubtype) with a null item subtype.

findHardware(DbControl, IdMethod, String, ItemSubtype) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Find a hardware with a given identifier.

findHybridization(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Find a hybridization with a given identifier.

findId - Static variable in class net.sf.basedb.clients.web.servlet.Download

findIndexName(String, Set<String>) - Method in class net.sf.basedb.core.dbengine.TableInfo

Check if there is an index with the same name or exactly the same set of columns.

findItemSubtype(DbControl, Item, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Try to find subtype from the given file data.

findItemSubtype(DbControl, IdMethod, Item, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Find an item subtype with a given identifier.

findKit(DbControl, IdMethod, String, ItemSubtype) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Find a kit with a given identifier.

findLabeledExtract(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Find a labled extract with a given identifier.

findMany - Static variable in class net.sf.basedb.clients.web.ModeInfo

findMaxBytes(Set<QuotaIndex>) - Method in class net.sf.basedb.core.data.QuotaIndex

Find the quota index entry in the given set and return the 'maxBytes' value.

findMethod(Class<?>, String, Class<?>...) - Static method in class net.sf.basedb.util.ClassUtil

Find a method in a clazz with the given name that takes the given list of arguments.

findOne - Static variable in class net.sf.basedb.clients.web.ModeInfo

findOtherUnit(Session, String) - Method in class net.sf.basedb.core.Unit

Find the unit with a given symbol that has the same quantity as this unit.

findParticipant(BioPlateData) - Method in class net.sf.basedb.core.BioPlateEvent

Find the participant object for the given bioplate.

findPermissionTemplate(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Find a permission template with a given identifier.

findPhysicalBioAssay(DbControl, IdMethod, String, ItemSubtype) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Find a physical bioassay with a given identifier.

findPlateGeometry(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Find a plate geometry with a given identifier.

findPlatform(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Find a platform with a given identifier.

findPlugins(DbControl, GuiContext, File, String, PluginDefinition) - Static method in class net.sf.basedb.util.AutoDetectFileFormat

Find all plugins with configurations which can import the specified file.

findProjectSpecific - Variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager

findProjectSpecificAnnotation(Annotation, int) - Method in class net.sf.basedb.core.ProjectSpecificAnnotationsManager

Find a project-specific annotation for a given default annotation.

findProtocol(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Same as AbstractItemImporter.findProtocol(DbControl, IdMethod, String, ItemSubtype) with a null item subtype.

findProtocol(DbControl, IdMethod, String, ItemSubtype) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Find a protocol with a given identifier.

findRange - Static variable in class net.sf.basedb.clients.web.servlet.Download

findRawDataType(DbControl, Platform, PlatformVariant, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Find a matching raw data type.

findReferencedItem(DbControl, IdMethod, ItemQuery<T>, String, int, boolean) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Find a referenced item.

findReferencedItemWithSubtype(DbControl, IdMethod, ItemQuery<T>, String, ItemSubtype, boolean) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Find a referenced item with a subtype.

findReporter - Variable in class net.sf.basedb.core.RawDataBatcher

A query to find reporters by the external id.

findReporter - Variable in class net.sf.basedb.core.ReporterBatcher

A query to find reporters by the external id.

findResource(String) - Method in class net.sf.basedb.util.JarClassLoader

findResource(String) - Method in class net.sf.basedb.util.JarClassLoader.JarClassLoaderProxy

findResources(String) - Method in class net.sf.basedb.util.JarClassLoader

findResources(String) - Method in class net.sf.basedb.util.JarClassLoader.JarClassLoaderProxy

findSample(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Same as AbstractItemImporter.findSample(DbControl, IdMethod, String, ItemSubtype) with a null subtype.

findSample(DbControl, IdMethod, String, ItemSubtype) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Find a sample with a given identifier.

findSetterMethod(String, Class<?>) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory

Find a setter method for the specified parameter.

findSoftware(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Same as AbstractItemImporter.findSoftware(DbControl, IdMethod, String, ItemSubtype) with a null item subtype.

findSoftware(DbControl, IdMethod, String, ItemSubtype) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Find a software with a given identifier.

findTag(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Same as AbstractItemImporter.findTag(DbControl, IdMethod, String, ItemSubtype) with a null item subtype.

findTag(DbControl, IdMethod, String, ItemSubtype) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Find a tag with a given identifier.

findTargetItem(String, String, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

findUnit(int, String) - Method in class net.sf.basedb.util.units.UnitCache

Finds a unit with a given symbol for a given quantity.

findUnit(String, String) - Method in class net.sf.basedb.util.units.UnitCache

Finds a unit with a given symbol for a given quantity.

findUnit(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Find a unit with a given identifier.

findUnit(Quantity, String) - Method in class net.sf.basedb.util.units.UnitCache

Finds a unit with a given symbol for a given quantity.

findUsers(String, QueryParameter...) - Method in class net.sf.basedb.core.AuthenticationContext

Find users in the database using a "free" restriction.

findValue(String, boolean, boolean) - Method in class net.sf.basedb.core.AnnotationType

This method should be used on enumerated string annotation types to find a matching predefined string value, optionally ignoring case and white-space.

findVariant(DbControl, Platform, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Find a platform variant with a given identifier.

findWell(int, int, int) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter

findWhat(StaleStateException) - Static method in exception net.sf.basedb.core.ItemModifiedException

FINGERPRINT_LENGTH - Static variable in class net.sf.basedb.core.data.FileServerData

FINGERPRINT_LENGTH - Static variable in class net.sf.basedb.core.FileServer

The length of the SSH fingerprint that can be stored in the database.

FINGERPRINT_PATTERN - Static variable in class net.sf.basedb.core.FileServer

Deprecated.

In 3.11, use FileServer.MD5_FINGERPRINT_PATTERN instead

FINGERPRINT_TYPE_MD5 - Static variable in class net.sf.basedb.core.FileServer

The fingerprint is a MD5 fingprint.

FINGERPRINT_TYPE_SHA256 - Static variable in class net.sf.basedb.core.FileServer

The fingerprint is a SHA256 fingprint.

fingerprintType - Variable in class net.sf.basedb.core.data.FileServerData

finish(Throwable) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

Called once when all files has been imported or when exiting due to an error.

finish(Throwable) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter

Commit/rollback transaction if needed.

finishedFileSize - Variable in class net.sf.basedb.plugins.AbstractFlatFileImporter

firstAssayFieldIndex - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo

firstColumn - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo

FirstPassSectionSpotsParser - Class in net.sf.basedb.util.importer.spotdata

Parses a 'spots' section of a BASEfile with bioassay set spot data.

FirstPassSectionSpotsParser(DbControl, BaseFileInfo, BioAssaySet) - Constructor for class net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser

Creates a new 'section spot' parser for the first pass.

firstResult - Variable in class net.sf.basedb.core.AbstractQuery

The index of the first result that should be returned by the query.

firstRow - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo

fitFraction - Variable in class net.sf.basedb.plugins.LowessNormalization.CallableWorker

fitFractionParameter - Static variable in class net.sf.basedb.plugins.LowessNormalization

Fix - Class in net.sf.basedb.util.overview

Holds information about a suggested fix to a failure.

Fix(String, BasicItem) - Constructor for class net.sf.basedb.util.overview.Fix

Create a new suggested fix for an item.

Fix(String, BasicItem, Annotation) - Constructor for class net.sf.basedb.util.overview.Fix

Create a new suggested fix for the annotation of an item.

Fix(String, BasicItem, AnnotationType, boolean) - Constructor for class net.sf.basedb.util.overview.Fix

Create a new suggested fix for the annotation of an item.

Fix(String, BasicItem, DataFileType) - Constructor for class net.sf.basedb.util.overview.Fix

Fix(String, BasicItem, FileSetMember) - Constructor for class net.sf.basedb.util.overview.Fix

FixDerivedBioAssayParentsRecursivelyAction(DbControl) - Constructor for class net.sf.basedb.core.DerivedBioAssay.FixDerivedBioAssayParentsRecursivelyAction

FixedButtonFactory - Class in net.sf.basedb.clients.web.extensions.toolbar

A simple implementation of a toolbar button action factory that creates the same fixed button for all users not using any context information.

FixedButtonFactory() - Constructor for class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory

Create a new factory instance.

FixedMenuItemFactory - Class in net.sf.basedb.clients.web.extensions.menu

A simple implementation of a menu item action factory that creates the same fixed menu item for all users not using any context information.

FixedMenuItemFactory() - Constructor for class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

Create a new factory instance.

FixedSkinActionFactory - Class in net.sf.basedb.clients.web.extensions.skin

A simple action factory implementation that always include the given skin on all pages.

FixedSkinActionFactory() - Constructor for class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory

Create a new factory instance.

FixedSkinActionFactory.MySkinAction - Class in net.sf.basedb.clients.web.extensions.skin

FixedStartPageFactory - Class in net.sf.basedb.clients.web.extensions.startpage

A simple start page action factory.

FixedStartPageFactory() - Constructor for class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory

Create a new factory instance.

FixedTabFactory - Class in net.sf.basedb.clients.web.extensions.tabcontrol

A simple implementation of a tab action factory that creates the same fixed tab for all users not using any context information.

FixedTabFactory() - Constructor for class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory

Create a new factory instance.

fixes - Variable in class net.sf.basedb.util.overview.Failure

fixPaths(Presets.Preset) - Method in class net.sf.basedb.util.extensions.manager.Settings

Fix paths in older config files.

fixSomeMoreThings(Metadata) - Static method in class net.sf.basedb.core.HibernateUtil

Other things that we may have to fix before the final build.

fixString(String) - Method in class net.sf.basedb.util.parser.FlatFileParser.Data

Fix the value string according to options for 'emptyIsNull', 'nullIsNull', etc.

fixUnitSymbolColumnDefinition(Element) - Static method in class net.sf.basedb.core.HibernateUtil

Fixes the definition of the UnitSymbols.symbol column so that it is case-sensitive.

fkColumns - Variable in class net.sf.basedb.core.dbengine.TableInfo.ForeignKeyInfo

flags - Variable in class net.sf.basedb.clients.web.formatter.NiceFormatter

FlatFileParser - Class in net.sf.basedb.util.parser

This class can be used to parse data from flat text files and from Excel workbooks in xlsx format.

FlatFileParser() - Constructor for class net.sf.basedb.util.parser.FlatFileParser

Create a new FlatFileParser object.

FlatFileParser.Data - Class in net.sf.basedb.util.parser

This class holds data about a line parsed by the FlatFileParser.hasMoreData() method.

FlatFileParser.ExcelData - Class in net.sf.basedb.util.parser

Subclass that is used to return data when the source file is an Excel file.

FlatFileParser.Line - Class in net.sf.basedb.util.parser

This class holds data about a line parsed by the FlatFileParser.parseHeaders() method.

FlatFileParser.LineType - Enum Class in net.sf.basedb.util.parser

Represents the type of a line matched or unmatched by the parser.

FLOAT - Enum constant in enum class net.sf.basedb.core.Type

Float type.

FLOAT - Enum constant in enum class net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType

FLOAT - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper

FloatConverter - Class in net.sf.basedb.util.jep.convert

Convert a Number constant to a Query API Expression from the float value.

FloatConverter() - Constructor for class net.sf.basedb.util.jep.convert.FloatConverter

FloatExpression - Class in net.sf.basedb.core.query

A constant float expression.

FloatExpression(float) - Constructor for class net.sf.basedb.core.query.FloatExpression

FloatParameterType - Class in net.sf.basedb.core

This class represent a parameter type that is a float.

FloatParameterType() - Constructor for class net.sf.basedb.core.FloatParameterType

Create a new float parameter type, without any limits and allowing null values.

FloatParameterType(Float, Float, Float, boolean) - Constructor for class net.sf.basedb.core.FloatParameterType

Create a new float parameter type.

FloatParameterType(Float, Float, Float, boolean, int, int, int, List<Float>) - Constructor for class net.sf.basedb.core.FloatParameterType

FloatParameterValueData - Class in net.sf.basedb.core.data

Float parameter value.

FloatParameterValueData() - Constructor for class net.sf.basedb.core.data.FloatParameterValueData

FloatParameterValueData(Float...) - Constructor for class net.sf.basedb.core.data.FloatParameterValueData

FloatWriter - Class in net.sf.basedb.core.migrate

Database-independent writer implementation that writes double values from a result set.

FloatWriter(ResultSet, int, Writer, char[]) - Constructor for class net.sf.basedb.core.migrate.FloatWriter

FLOW_RATE - Static variable in class net.sf.basedb.core.Quantity

The id for the Quantity object representing flow rate.

flush() - Method in class net.sf.basedb.core.AnnotationBatcher

Flush the batchers.

flush() - Method in class net.sf.basedb.core.AnnotationBatcher.UpdateBatcher

Flush and execute the statements added to the batch.

flush() - Method in class net.sf.basedb.core.BasicBatcher

flush() - Method in interface net.sf.basedb.core.Batcher

Flush the batcher and send all remaining items in memory to the database.

flush() - Method in class net.sf.basedb.core.FilterBatcher

flush() - Method in class net.sf.basedb.core.hibernate.SessionWrapper

flush() - Method in class net.sf.basedb.core.LogControl

Flushes any batched changes to the database.

flush() - Method in class net.sf.basedb.core.MappingBatcher

flush() - Method in class net.sf.basedb.core.MigrateRbaToDba

Flush all batchers

flush() - Method in class net.sf.basedb.core.plugin.ExportOutputStream

flush() - Method in class net.sf.basedb.core.PositionBatcher

flush() - Method in class net.sf.basedb.core.PositionExtraValueBatcher

flush() - Method in class net.sf.basedb.core.ReporterCloneBatcher

flush() - Method in class net.sf.basedb.core.SpotBatcher

flush() - Method in class net.sf.basedb.core.SpotExtraValueBatcher

flush(Session) - Static method in class net.sf.basedb.core.HibernateUtil

Flush all changed objects to the database.

flushDelete() - Method in class net.sf.basedb.core.BasicBatcher

Flush the SQL delete command buffer.

flushInsert() - Method in class net.sf.basedb.core.BasicBatcher

Flush the SQL insert command buffer.

flushInsert() - Method in class net.sf.basedb.core.ReporterBatcher

Flush and clear the internal cache of external reporter id:s.

flushInternal() - Method in class net.sf.basedb.core.ReporterCloneBatcher

FlushSessionAction(Session) - Constructor for class net.sf.basedb.core.ServiceSessionControl.FlushSessionAction

flushUpdate() - Method in class net.sf.basedb.core.BasicBatcher

Flush the SQL insert command buffer.

FOLDER - Enum constant in enum class net.sf.basedb.util.overview.Node.Type

FORCE - Enum constant in enum class net.sf.basedb.core.ItemContext.AddFilter

Always add a filter, overwriting an existing one.

FORCE - Static variable in class net.sf.basedb.core.Quantity

The id for the Quantity object representing force.

forceItemPermission() - Method in class net.sf.basedb.clients.web.ModeInfo

forceMimeType - Variable in class net.sf.basedb.clients.web.servlet.Download

forceStop - Variable in class net.sf.basedb.core.signal.ThreadSignalHandler

If TRUE, call Thread.stop() instead of Thread.interrupt()

forceUpdate - Variable in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor

ForeignKeyInfo(String, String) - Constructor for class net.sf.basedb.core.dbengine.TableInfo.ForeignKeyInfo

Create a new ForeignKeyInfo object.

foreignKeys - Variable in class net.sf.basedb.core.dbengine.TableInfo

forgetOldResults(ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.ProcessResults

Forget old processing results for the given file.

Form - Class in net.sf.basedb.clients.web.taglib.table

An alternative layout for tables which contains only one row.

Form() - Constructor for class net.sf.basedb.clients.web.taglib.table.Form

format - Variable in class net.sf.basedb.util.excel.ExcelValue

format - Variable in class net.sf.basedb.util.formatter.DateFormatter

format - Variable in class net.sf.basedb.util.formatter.IntegerFormatter

format - Variable in class net.sf.basedb.util.formatter.NumberFormatFormatter

format(Boolean) - Method in class net.sf.basedb.util.formatter.BooleanFormatter

format(Enum<T>) - Method in class net.sf.basedb.util.formatter.EnumFormatter

format(Integer) - Method in class net.sf.basedb.core.log.ChangeTypeFormatter

format(Integer) - Method in class net.sf.basedb.util.formatter.ItemTypeFormatter

format(Integer) - Method in class net.sf.basedb.util.formatter.ValueTypeFormatter

format(Integer) - Method in class net.sf.basedb.util.formatter.WellCoordinateFormatter

format(Number) - Method in class net.sf.basedb.clients.web.formatter.ColorFormatter

format(Number) - Method in class net.sf.basedb.util.formatter.AdaptiveNumberFormatter

format(Number) - Method in class net.sf.basedb.util.formatter.IntegerFormatter

format(Number) - Method in class net.sf.basedb.util.formatter.NumberFormatFormatter

format(Number) - Method in class net.sf.basedb.util.formatter.NumberFormatter

format(Object) - Method in class net.sf.basedb.util.formatter.MultiFormatter

format(String) - Method in class net.sf.basedb.clients.web.formatter.NiceFormatter

format(String) - Method in class net.sf.basedb.clients.web.formatter.StringFormatter

format(Collection<I>) - Method in class net.sf.basedb.util.formatter.CollectionFormatter

format(Date) - Method in class net.sf.basedb.util.formatter.DateFormatter

format(BasicItem) - Method in class net.sf.basedb.clients.web.formatter.AutoItemExportFormatter

format(BasicItem) - Method in class net.sf.basedb.clients.web.formatter.AutoLinkFormatter

format(BioMaterialEventSource) - Method in class net.sf.basedb.clients.web.plugins.BioMaterialEventSourceFormatter

format(File) - Method in class net.sf.basedb.clients.web.formatter.LinkedFileFormatter

format(File) - Method in class net.sf.basedb.util.formatter.FilePathFormatter

format(FileSet) - Method in class net.sf.basedb.clients.web.formatter.DataFileFormatter

Lists the name of all member files in the file set that are of the configured file type.

format(Identifiable) - Method in class net.sf.basedb.util.formatter.IdentifiableFormatter

format(Nameable) - Method in class net.sf.basedb.clients.web.formatter.LinkedItemFormatter

format(Nameable) - Method in class net.sf.basedb.util.formatter.NameableFormatter

format(PropertyFilter) - Method in class net.sf.basedb.util.formatter.PropertyFilterFormatter

format(ExportableField) - Method in class net.sf.basedb.util.export.spotdata.ExportableFieldFormatter

format(T) - Method in class net.sf.basedb.clients.web.formatter.ExtendedPropertyFormatter

format(T) - Method in interface net.sf.basedb.util.formatter.Formatter

Format a value by converting it to a string.

format(T) - Method in class net.sf.basedb.util.formatter.LookupFormatter

format(T) - Method in class net.sf.basedb.util.formatter.PrefixSuffixFormatter

format(T) - Method in class net.sf.basedb.util.formatter.ToStringFormatter

FORMAT - Static variable in class net.sf.basedb.clients.web.plugins.SimpleExport

FORMAT_BASEFILE_MATRIX - Static variable in class net.sf.basedb.plugins.BaseFileExporterPlugin

FORMAT_BASEFILE_SERIAL - Static variable in class net.sf.basedb.plugins.BaseFileExporterPlugin

formatBytes(Long) - Static method in class net.sf.basedb.util.Values

Formats a value using units of bytes, kilobytes, megabytes or gigabytes.

formatBytes(Long, int) - Static method in class net.sf.basedb.util.Values

Formats a value using units of bytes, kilobytes, megabytes or gigabytes.

formatDate(Date) - Static method in class net.sf.basedb.core.DateUtil

Formats a date in yyyy-MM-dd format.

formatLineBreaks(String) - Static method in class net.sf.basedb.clients.web.util.HTML

Finds all linebreaks in a string and replaces them with a <br> tag, except that leading and trailing linebreaks will be removed.

formatMessage(String, Object...) - Static method in class net.sf.basedb.util.Values

Insert the values of parameters into a template message.

formatNumber(Float, int) - Static method in class net.sf.basedb.util.Values

Formats a decimal number with the specified number of decimals.

formatNumber(Float, int, String) - Static method in class net.sf.basedb.util.Values

Formats a decimal number with the specified number of decimals and optionally adding a unit.

formatter - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

formatter - Variable in class net.sf.basedb.clients.web.plugins.ExportedProperty

formatter - Variable in class net.sf.basedb.clients.web.taglib.table.Cell

formatter - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef

formatter - Variable in class net.sf.basedb.clients.web.taglib.table.TableColumn

formatter - Variable in class net.sf.basedb.util.export.spotdata.AnnotationAssayField

formatter - Variable in class net.sf.basedb.util.export.spotdata.AssayPropertyField

formatter - Variable in class net.sf.basedb.util.export.spotdata.JepDynamicField

formatter - Variable in class net.sf.basedb.util.export.spotdata.SimpleDynamicField

formatter - Variable in class net.sf.basedb.util.formatter.MultiFormatter

Formatter<T> - Interface in net.sf.basedb.util.formatter

A Formatter formats an object to a string suitable for output in a client application.

formatterClass - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

FormatterFactory - Class in net.sf.basedb.clients.web.formatter

Factory class for creating formatters for various data types.

FormatterFactory() - Constructor for class net.sf.basedb.clients.web.formatter.FormatterFactory

formatters - Variable in class net.sf.basedb.util.export.TableWriter

formatters - Variable in class net.sf.basedb.util.formatter.MultiFormatter

FormatterSettings - Class in net.sf.basedb.clients.web.formatter

This is autility class for getting and setting formatter-related settings for the logged in user.

FormatterSettings() - Constructor for class net.sf.basedb.clients.web.formatter.FormatterSettings

formatTime(long) - Static method in class net.sf.basedb.util.Values

Formats a number of seconds to a more proper time format.

formatTimestamp(Date) - Static method in class net.sf.basedb.core.DateUtil

Formats a timestamp in yyyy-MM-dd HH:mm:ss format.

formatType - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter

FormatType() - Constructor for enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.FormatType

formName - Variable in class net.sf.basedb.clients.web.fileupload.UploadedFile

formula(Formula, String, Formatter<?>) - Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory

Create a JEP dynamic field that exports the result of the JEP expression in a formula.

Formula - Class in net.sf.basedb.core

This class represents a formula.

Formula(FormulaData) - Constructor for class net.sf.basedb.core.Formula

FORMULA - Enum constant in enum class net.sf.basedb.core.Item

The item is a Formula

Formula.AverageMethod - Enum Class in net.sf.basedb.core

The average method used for the values of this formula.

Formula.Parser - Enum Class in net.sf.basedb.core

The parser used to parse the formula.

Formula.Type - Enum Class in net.sf.basedb.core

The type of formula indicats in which situations it can be used.

FormulaData - Class in net.sf.basedb.core.data

This class holds information about a formula used in the analysis of raw data and bioassay sets.

FormulaData() - Constructor for class net.sf.basedb.core.data.FormulaData

formulaEval - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo

FormulaFilter - Class in net.sf.basedb.plugins

This plugin provides methods to filter a bioassayset based on formulas entered by the user.

FormulaFilter() - Constructor for class net.sf.basedb.plugins.FormulaFilter

Constructor should be empty.

formulaParameter - Variable in class net.sf.basedb.plugins.IntensityCalculatorPlugin

formulaQuery - Variable in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter

formulas - Variable in class net.sf.basedb.core.data.FormulaData

formulas - Variable in class net.sf.basedb.core.RawDataType

formulaToExpression(String, JepFunction...) - Static method in class net.sf.basedb.util.jep.Jep

Convert JEP expression to a Query API Expression.

formulaToRestriction(String, JepFunction...) - Static method in class net.sf.basedb.util.jep.Jep

Convert JEP expression to a Query API Restriction.

formulaType - Variable in class net.sf.basedb.plugins.IntensityCalculatorPlugin

FORWARD - Enum constant in enum class net.sf.basedb.util.overview.node.ChildNodeDirection

Child nodes should be loaded in the forward-loading direction.

ForwardingSignalHandler - Class in net.sf.basedb.core.signal

A signal handler implementation that forwards the signal to another signal transporter.

ForwardingSignalHandler(SignalTransporter) - Constructor for class net.sf.basedb.core.signal.ForwardingSignalHandler

Create a new forwarding signal handler.

forwardSignalMessageIfNeeded(String) - Method in class net.sf.basedb.core.signal.SocketSignalReceiver

If the message has forwarding information, forward the message to the other host.

forwardTo - Variable in class net.sf.basedb.core.signal.ForwardingSignalHandler

The signal transporter to forward signals to.

forwardTo - Variable in class net.sf.basedb.core.signal.ProgressReporterSignalHandler

Original progress reporter that progress updates should be forwarded to.

forwardTo(ProgressReporter) - Method in class net.sf.basedb.core.signal.ProgressReporterSignalHandler

Set the progress reporter that progress information should be forwarded to.

FPKM_TRACKING - Static variable in class net.sf.basedb.core.DataFileType

The external ID for the file type representing a FPKM tracking file.

FRACTION - Static variable in class net.sf.basedb.core.Quantity

The id for the Quantity object representing fractions.

freeWells - Variable in class net.sf.basedb.core.data.BioPlateData

freezer - Variable in class net.sf.basedb.core.data.BioPlateData

FREEZER - Static variable in class net.sf.basedb.core.Hardware

The id for the HardwareType object representing a freezer.

FREQUENCY - Static variable in class net.sf.basedb.core.Quantity

The id for the Quantity object representing frequency.

from - Variable in class net.sf.basedb.core.AnyToAny

from - Variable in class net.sf.basedb.core.data.MessageData

from(String...) - Static method in class net.sf.basedb.util.Enumeration

Create a new enumeration from a list strings.

FROM - Enum constant in enum class net.sf.basedb.core.query.QuerySection

fromClass(Class<?>) - Static method in enum class net.sf.basedb.core.Item

Get the Item object when you know either the item or data class.

fromDataClass(Class<? extends BasicData>) - Static method in enum class net.sf.basedb.core.Item

Get the Item object when you know the data class.

fromDataObject(BasicData) - Static method in enum class net.sf.basedb.core.Item

Get the Item object when you have a data layer object.

fromDeniedInt(int) - Static method in enum class net.sf.basedb.core.Permission

Convert an integer value to a set of denied permissions.

fromHex(String) - Static method in class net.sf.basedb.util.ColorGenerator

Convert a hexadecimal color string such as one used in HTML to a Color object.

fromHibernateType(Type) - Static method in enum class net.sf.basedb.core.Type

Try to find a matching Type instance given a Hibernate Type object.

fromId - Variable in class net.sf.basedb.core.data.AnyToAnyData

fromId - Variable in class net.sf.basedb.core.data.MessageData

fromInherited - Variable in class net.sf.basedb.util.overview.Fix

fromInt(int) - Static method in enum class net.sf.basedb.core.Include

Convert an integer value to a set of includes.

fromInt(int) - Static method in enum class net.sf.basedb.core.Permission

Convert an integer value to a set of granted permissions.

fromItemClass(Class<? extends BasicItem>) - Static method in enum class net.sf.basedb.core.Item

Get the Item object when you know the item class.

fromItems(Collection<? extends Nameable>, String) - Static method in class net.sf.basedb.util.Enumeration

Create a new enumeration from a list of basic items.

fromItems(Collection<? extends Nameable>, String, String) - Static method in class net.sf.basedb.util.Enumeration

Create a new enumeration from a list of basic items.

fromJson(JSONObject) - Static method in class net.sf.basedb.util.GeoLocation

Convert JSON data from freegeoip to a GeoLocation instance.

fromOther(double, Unit) - Method in class net.sf.basedb.core.Unit

Convert a value from another unit to this unit.

fromReferenceUnit(double) - Method in class net.sf.basedb.core.Unit

Convert a value from the reference unit to this unit.

fromString(String) - Static method in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section

fromType - Variable in class net.sf.basedb.core.AnyToAny.FastLinkLoader

fromType - Variable in class net.sf.basedb.core.data.AnyToAnyData

fromType(String) - Static method in class net.sf.basedb.util.formatter.BooleanFormatter

Create a formatter for boolean values.

fromValue(int) - Static method in enum class net.sf.basedb.core.BioMaterialEvent.Type

Get the BioMaterialEvent.Type object when you know the integer code.

fromValue(int) - Static method in enum class net.sf.basedb.core.BioWell.LockMode

Get the Lock mode object when you know the integer code.

fromValue(int) - Static method in enum class net.sf.basedb.core.ExtraValue.CoordinateType

Get the CoordinateType object when you know the integer code.

fromValue(int) - Static method in enum class net.sf.basedb.core.FeatureIdentificationMethod

Get the FeatureIdentificationMethod object when you know the integer code.

fromValue(int) - Static method in enum class net.sf.basedb.core.Formula.AverageMethod

Get the Formula.AverageMethod object when you know the integer code.

fromValue(int) - Static method in enum class net.sf.basedb.core.Formula.Parser

Get the Formula.Parser object when you know the integer code.

fromValue(int) - Static method in enum class net.sf.basedb.core.Formula.Type

Get the Formula.Type object when you know the integer code.

fromValue(int) - Static method in enum class net.sf.basedb.core.IntensityTransform

Get the SpotDataTransform object when you know the integer code.

fromValue(int) - Static method in enum class net.sf.basedb.core.Item

Get the Item object when you know the integer code.

fromValue(int) - Static method in enum class net.sf.basedb.core.ItemContext.SortDirection

Get the SortDirection object when you know the integer code.

fromValue(int) - Static method in enum class net.sf.basedb.core.Job.ExecutionTime

Get the Job.Status object when you know the integer code.

fromValue(int) - Static method in enum class net.sf.basedb.core.Job.Status

Get the Job.Status object when you know the integer code.

fromValue(int) - Static method in enum class net.sf.basedb.core.Job.Type

Get the Job.Status object when you know the integer code.

fromValue(int) - Static method in enum class net.sf.basedb.core.Location

Get the Location object when you know the integer code.

fromValue(int) - Static method in enum class net.sf.basedb.core.log.ChangeType

Get the change type corresponding to the given numerical value.

fromValue(int) - Static method in enum class net.sf.basedb.core.Operator

Get the Operator object when you know the integer code.

fromValue(int) - Static method in enum class net.sf.basedb.core.plugin.GuiContext.Type

Get the GuiContext.Type object when you know the integer code.

fromValue(int) - Static method in enum class net.sf.basedb.core.plugin.Plugin.MainType

fromValue(int) - Static method in enum class net.sf.basedb.core.Type

Get the Type object when you know the integer code.

fromValue(String) - Static method in enum class net.sf.basedb.core.Type

Get the Type object when you know the string value.

fu - Variable in class net.sf.basedb.clients.web.fileupload.UploadedFile

FULL - Enum constant in enum class net.sf.basedb.core.ItemList.SynchronizeOption

Synchronize the members so that it contains all of the items matching the filter and no items not matching the filter.

fullFieldName - Variable in class net.sf.basedb.util.overview.extensions.ReflectValidationRuleActionFactory

function(String) - Method in class net.sf.basedb.util.formatter.PropertyFilterFormatter

functions - Static variable in class net.sf.basedb.util.jep.Jep

FunctionSafeJep - Class in net.sf.basedb.util.jep

Extension to the JEP parser that provides better error handling for unknown functions.

FunctionSafeJep() - Constructor for class net.sf.basedb.util.jep.FunctionSafeJep

Create a new function-safe JEP parser.

FunctionSafeJep.SafeFunctionTable - Class in net.sf.basedb.util.jep

Function table implementation that pretends that all possible functions exists, but sends an error message if someone tries to use a function that doesn't really exists.

FunctionSafeJep.UnknownFunction - Class in net.sf.basedb.util.jep

Represents an unknown function that appears in an expression.

FutureItem(Class<T>, Query<T>) - Constructor for class net.sf.basedb.core.QueryExecutor.FutureItem

FutureResultSet(PreparedStatement) - Constructor for class net.sf.basedb.core.QueryExecutor.FutureResultSet

FutureScrollIterator(Query<T>) - Constructor for class net.sf.basedb.core.QueryExecutor.FutureScrollIterator

FutureUpdate(PreparedStatement) - Constructor for class net.sf.basedb.core.QueryExecutor.FutureUpdate

FuzzyMatch(String, String, double) - Constructor for class net.sf.basedb.util.fuzzy.StringMatcher.FuzzyMatch

G

GalExporter - Class in net.sf.basedb.plugins

Exports an array design with features to a GAL file.

GalExporter() - Constructor for class net.sf.basedb.plugins.GalExporter

GB - Static variable in class net.sf.basedb.util.Values

GENE_ID - Static variable in class net.sf.basedb.util.gtf.GtfInputStream.Attribute

geneAveragesParameter - Variable in class net.sf.basedb.plugins.Base1PluginExecuter

If the data should be exported averaged per gene.

geneIdIndex - Variable in class net.sf.basedb.util.gtf.GtfInputStream

generateCFPlot(BioAssay, String, String) - Method in class net.sf.basedb.clients.web.servlet.PlotServlet

Generates a correction-factor plot, which is plotting the MA-data for the parent together with the difference in M between the parent and child.

generateDefaultName(FilePacker, Directory, Collection<Nameable>) - Method in class net.sf.basedb.plugins.PackedFileExporter

Generate a default name without a path for the packed file.

generateDefaultPath(FilePacker, Directory, Collection<Nameable>) - Method in class net.sf.basedb.plugins.PackedFileExporter

Generate a default path for the packed file.

generatedFiles - Variable in class net.sf.basedb.util.bfs.AbstractFilenameGenerator

generateExportTitle(String) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

Generates an export title using target item type and subtype as prefix.

generateRandomId(int) - Static method in class net.sf.basedb.core.Application

Generate a random id.

generateSignalMessage(Signal) - Method in class net.sf.basedb.core.signal.AbstractSignalTransporter

Generate a signal message string for the given signal.

generateSubtitle() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

generateTitle(String) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

Generates a title using target item type and subtype as prefix.

generateTitle(String, String) - Method in class net.sf.basedb.clients.web.ModeInfo

generateTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

Generates a tooltip using target item type and subtype as prefix.

generators - Variable in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean

GENERIC - Static variable in class net.sf.basedb.core.BioPlateEventType

The system ID for "Generic" event type.

GENERIC - Static variable in class net.sf.basedb.core.Platform

The external id for the Generic platform.

GENERIC_EXTRAVALUE_DATA - Static variable in class net.sf.basedb.core.DataFileType

The external ID for the file type representing generic analysed extra value data.

GENERIC_PRINT_MAP - Static variable in class net.sf.basedb.core.DataFileType

The external ID for the file type representing a generic print map (array design layout) of any type.

GENERIC_RAW_DATA - Static variable in class net.sf.basedb.core.DataFileType

The external ID for the file type representing a generic raw data file of any type.

GENERIC_REPORTER_MAP - Static variable in class net.sf.basedb.core.DataFileType

The external ID for the file type representing a generic reporter map (array design layout) of any type.

GENERIC_SPOT_DATA - Static variable in class net.sf.basedb.core.DataFileType

The external ID for the file type representing generic analysed spot data.

GenericBaseDataWriterFactory<T> - Class in net.sf.basedb.util.bfs

Generic implementation of a data writer factory that create files in the BASE file system.

GenericBaseDataWriterFactory(DbControl, Directory, FilenameGenerator<T>) - Constructor for class net.sf.basedb.util.bfs.GenericBaseDataWriterFactory

Create a new factory that creates files in the given directory.

GenericDiskDataWriterFactory<T> - Class in net.sf.basedb.util.bfs

Generic implementation of a data writer factory that create files on the local file system.

GenericDiskDataWriterFactory(File, FilenameGenerator<T>) - Constructor for class net.sf.basedb.util.bfs.GenericDiskDataWriterFactory

Create a new factory that creates files in the given directory.

GenericExtraFileImporter - Class in net.sf.basedb.util.bfs

Extra file importer implementation that imports file to a specified directory in the BASE file system.

GenericExtraFileImporter(DbControl, Directory, boolean) - Constructor for class net.sf.basedb.util.bfs.GenericExtraFileImporter

Create a new extra file importer.

GenericIntensityParser - Class in net.sf.basedb.util.importer.spotdata

Generic spot intensity parser implementation that looks for 'intensity1', ..., 'intensityN' data columns for any number of channels.

GenericIntensityParser(int) - Constructor for class net.sf.basedb.util.importer.spotdata.GenericIntensityParser

Creates a new parser for the specified number of channels.

GenericOverview - Class in net.sf.basedb.util.overview

Implementation for holding a generic overview of items.

GenericOverview(DbControl, BasicItem, Project) - Constructor for class net.sf.basedb.util.overview.GenericOverview

Create a new generic overview.

genericType - Variable in class net.sf.basedb.core.data.DataFileTypeData

gensalt() - Static method in class net.sf.basedb.util.bcrypt.BCrypt

Generate a salt for use with the BCrypt.hashpw() method, selecting a reasonable default for the number of hashing rounds to apply

gensalt(int) - Static method in class net.sf.basedb.util.bcrypt.BCrypt

Generate a salt for use with the BCrypt.hashpw() method

gensalt(int, SecureRandom) - Static method in class net.sf.basedb.util.bcrypt.BCrypt

Generate a salt for use with the BCrypt.hashpw() method

GENSALT_DEFAULT_LOG2_ROUNDS - Static variable in class net.sf.basedb.util.bcrypt.BCrypt

GeoLocation - Class in net.sf.basedb.util

Utility class for geographic location.

GeoLocation() - Constructor for class net.sf.basedb.util.GeoLocation

GeoLocation.ResponseFilter - Class in net.sf.basedb.util

We only accept "200" status response, "application/json" content type and not more than 1K bytes (should be a lot less under normal operations).

GEOMETRIC_MEAN - Enum constant in enum class net.sf.basedb.core.Formula.AverageMethod

geometricMean(Expression) - Static method in class net.sf.basedb.core.query.Aggregations

Calculates the geometric mean of all values for an expression: new expression = EXP(AVG(LN(e))).

GeometricMeanExpression - Class in net.sf.basedb.core.query

Calculates the geometric mean of an expression: EXP(AVG(LN(e)))

GeometricMeanExpression(Expression) - Constructor for class net.sf.basedb.core.query.GeometricMeanExpression

geometryQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

get - Variable in class net.sf.basedb.util.uri.http.HttpConnectionManager.TimeoutTimer

get(char) - Static method in enum class net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType

get(int) - Method in class net.sf.basedb.core.ItemResultList

Get a BasicItem derived object.

get(int) - Method in class net.sf.basedb.util.parser.FlatFileParser.Data

Deprecated.

In 3.15, use FlatFileParser.Data.getString(int) instead or one of the other getXxx() method to return a given data type directly

get(int, int) - Method in interface net.sf.basedb.core.query.SqlResultList

get(int, String) - Method in interface net.sf.basedb.core.query.SqlResultList

get(Class<E>, BasicData) - Method in class net.sf.basedb.core.ItemResultList

get(Class<T>, Serializable) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

get(Class<T>, Serializable, LockMode) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

get(Class<T>, Serializable, LockOptions) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

get(Class, Serializable) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

get(Class, Serializable, LockMode) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

get(Object) - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter

Get the value of the extended property.

get(Object) - Method in class net.sf.basedb.util.ClassLocal

Get the object associated with the class of the specified instance.

get(Object) - Method in class net.sf.basedb.util.formatter.LookupFormatter

Get registered lookup value for a given key

get(String) - Method in class net.sf.basedb.clients.web.extensions.skin.ImageRemapper

Get the remapped image for the given source image.

get(String) - Static method in class net.sf.basedb.clients.web.ModeInfo

get(String, Serializable) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

get(String, Serializable) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

get(String, Serializable, LockMode) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

get(String, Serializable, LockMode) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

get(String, Serializable, LockOptions) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

get(JspContext) - Static method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerUtil

Get an existing instance that is stored in the given JSP context.

get(DbControl) - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Get an extension control object for managing the installed extensions.

get(DbControl) - Static method in class net.sf.basedb.core.DerivedBioAssay.FixDerivedBioAssayParentsRecursivelyAction

Get an instance tht handles the fixes for the given DbControl.

get(DbControl, MeasuredBioMaterialData) - Static method in class net.sf.basedb.core.MeasuredBioMaterial.RemainingQuantityAction

get(DbControl, ItemQuery<? extends E>...) - Static method in class net.sf.basedb.util.query.MultiQueryIterator

Create a new iterator for the given list of queries.

get(AnnotationUtil.AnnotatableWrapper) - Method in class net.sf.basedb.util.AnnotationUtil.Cache

get(TransformCache.CacheKey) - Method in class net.sf.basedb.util.listable.TransformCache

Get a cached entry if.

getAbout() - Method in interface net.sf.basedb.util.extensions.Extension

Get information about the extensions.

getAbout() - Method in class net.sf.basedb.util.extensions.ExtensionBean

getAbout() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile

Get information about the extensions in this file.

getAbout() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension

getAbout() - Method in class net.sf.basedb.util.extensions.xml.PluginInfo

Get information about the authors of the plug-in.

getAbsolutePath(String) - Static method in class net.sf.basedb.core.File

Convert a relative path back to an absolute file path.

getAbstract() - Method in class net.sf.basedb.core.data.ExperimentData

Get the abstract for this experiment.

getAbstract() - Method in class net.sf.basedb.core.Experiment

Get the abstract text for the publication for this experiment.

getAcceptedFile() - Method in class net.sf.basedb.util.fileset.SingleFileValidationAction

Get the file that was last accepted by the SingleFileValidationAction.acceptFile(FileSetMember) method.

getAction() - Method in class net.sf.basedb.clients.web.taglib.table.Table

getActionClass() - Method in interface net.sf.basedb.util.extensions.ExtensionPoint

Get the class object that represents the type of action that can be added to this extension point.

getActionClass() - Method in class net.sf.basedb.util.extensions.ExtensionPointBean

getActionClass() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint

getActionFactory() - Method in interface net.sf.basedb.util.extensions.Extension

Get the factory class for creating actions.

getActionFactory() - Method in class net.sf.basedb.util.extensions.ExtensionBean

getActionFactory() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension

getActionId() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

Get the action id from the expression.

getActions() - Method in class net.sf.basedb.util.extensions.ExtensionContext

Call Extension.getActionFactory() and then ActionFactory.getActions(InvokationContext) on the returned factory.

getActions() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext

Always null, since this is an extension point context.

getActions() - Method in class net.sf.basedb.util.extensions.InvokationContext

Get the actions, or null if there is no current extension.

getActions(InvokationContext<? super A>) - Method in interface net.sf.basedb.util.extensions.ActionFactory

This method may be called one or several times for each request.

getActions(InvokationContext<? super OnSaveAction>) - Method in class net.sf.basedb.clients.web.extensions.edit.DebugOnSaveActionFactory

getActions(InvokationContext<? super ListColumnAction<I, V>>) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

getActions(InvokationContext<? super ListColumnAction<Annotatable, Object>>) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumnActionFactory

getActions(InvokationContext<? super ListColumnAction<BasicItem, Object>>) - Method in class net.sf.basedb.clients.web.extensions.list.AnyLinkColumnActionFactory

getActions(InvokationContext<? super LoginFormAction>) - Method in class net.sf.basedb.clients.web.extensions.login.PasswordLoginFormFactory

getActions(InvokationContext<? super MenuItemAction>) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

getActions(InvokationContext<? super MenuItemAction>) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

getActions(InvokationContext<? super OverviewPlotAction>) - Method in class net.sf.basedb.clients.web.extensions.plot.MAPlotFactory

getActions(InvokationContext<? super SectionAction>) - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory

getActions(InvokationContext<? super ServiceControllerAction>) - Method in class net.sf.basedb.clients.web.extensions.service.DummyService

getActions(InvokationContext<? super SkinAction>) - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory

getActions(InvokationContext<? super StartPageAction>) - Method in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory

getActions(InvokationContext<? super TabAction>) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory

getActions(InvokationContext<? super TabAction>) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory

getActions(InvokationContext<? super ButtonAction>) - Method in class net.sf.basedb.clients.web.extensions.fileviewer.ViewAndDownloadActionFactory

getActions(InvokationContext<? super ButtonAction>) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory

getActions(InvokationContext<? super ButtonAction>) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

getActions(InvokationContext<? super LogManagerFactory>) - Method in class net.sf.basedb.core.log.db.DbLogManagerFactory

getActions(InvokationContext<? super CdfValidationAction>) - Method in class net.sf.basedb.util.affymetrix.CdfValidationFactory

getActions(InvokationContext<? super CelValidationAction>) - Method in class net.sf.basedb.util.affymetrix.CelValidationFactory

getActions(InvokationContext<? super Action>) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory

getActions(InvokationContext<? super Action>) - Method in class net.sf.basedb.util.extensions.debug.ProxyActionFactory

getActions(InvokationContext<? super GtfValidationAction>) - Method in class net.sf.basedb.util.gtf.GtfValidationFactory

getActions(InvokationContext<? super ValidationRuleAction>) - Method in class net.sf.basedb.util.overview.extensions.ReflectValidationRuleActionFactory

getActions(InvokationContext<? super ConnectionManagerFactory>) - Method in class net.sf.basedb.util.uri.http.HttpConnectionManagerActionFactory

getActive() - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl

getActive(DbControl) - Static method in class net.sf.basedb.core.Project

Get the currently active project if any.

getActiveProjectId() - Method in class net.sf.basedb.core.data.JobData

The ID of the project that should be made active when running this job.

getActiveProjectId() - Method in class net.sf.basedb.core.Job

The ID of the project that should be made the active project while running this job.

getActiveProjectId() - Method in class net.sf.basedb.core.SessionControl

Get the id of the active project, or 0 if no project is active.

getActiveProjectName() - Method in class net.sf.basedb.core.SessionControl

Get the name of the active project, or null if no project is active.

getActiveProjectPermissions() - Method in class net.sf.basedb.core.SessionControl

Get the permissions that the logged in user has in the currently active project.

getActiveRoles() - Method in class net.sf.basedb.core.SessionControl

Get the id of all active roles where the logged in user is a member.

getActualCatalog() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration

The actual catalog that will be used by BASE.

getActualSchema() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration

The actual schema that will be used by BASE.

getActualUnit(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

Get the unit that is most relevant for this annotation.

getActualValues() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

Get the annotation values that are most relevant for this annotation.

getActualValues(UnitConverter, Type) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

Get the annotations values, optionally converted to some specific unit and type of values.

getAddFilter() - Method in class net.sf.basedb.clients.web.SubContext

getAddress() - Method in class net.sf.basedb.core.authentication.ExtraUserInformation

The postal address to the user.

getAddress() - Method in class net.sf.basedb.core.data.UserData

Get the address for the user, or null if unknown.

getAddress() - Method in class net.sf.basedb.core.User

Get the address for the user, or null if unknown.

getAdvancedAssayField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.AdvancedFieldConverter

Convert an expression to an assay field.

getAdvancedReporterField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.AdvancedFieldConverter

Convert an expression to a reporter field.

getAdvancedSpotField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.AdvancedFieldConverter

Convert an expression to a spot field.

getAffiliations() - Method in class net.sf.basedb.core.data.ExperimentData

Get the affiliations for this experiment.

getAffiliations() - Method in class net.sf.basedb.core.Experiment

Get the affiliations for this experiment.

getAge() - Method in class net.sf.basedb.core.DiskUsageStatistics.Summary

Get the age of this summary object since it was created in seconds.

getAge() - Method in class net.sf.basedb.util.jobagent.JobAgentInfo

Get the age in milliseconds of this object.

getAgent() - Method in class net.sf.basedb.clients.jobagent.handlers.AbstractCustomRequestHandler

getAgent() - Method in class net.sf.basedb.clients.jobagent.slotmanager.InternalSlotManager

Get the job agent this slot manager belongs to.

getAgentInfo(JobAgent) - Static method in class net.sf.basedb.core.JobAgent

Get a JobAgentInfo for a job agent.

getAlias() - Method in enum class net.sf.basedb.core.Item

Get the alias for this item, which is used in queries,

getAlias() - Method in class net.sf.basedb.core.query.AnnotationExpression

getAlias() - Method in class net.sf.basedb.core.query.ExpressionSelect

getAlias() - Method in interface net.sf.basedb.core.query.Select

Get the alias of the selected expression.

getAlias() - Method in class net.sf.basedb.core.RealTable

Get the alias of this table.

getAlias() - Method in enum class net.sf.basedb.core.VirtualTable

Get the alias of this table.

getAlias(int) - Method in class net.sf.basedb.core.RealTable

Get the alias of this table, using the ID of the item to make it unique.

getAlias(BasicItem) - Method in class net.sf.basedb.core.RealTable

Get the alias of this table, using the ID of the item to make it unique.

getAll() - Static method in class net.sf.basedb.core.ClonableProperty

Get a list containing cloned property representation for all static and extended properties.

getAllAnnotatableParentItems(DbControl, Annotatable, Filter<Annotatable>) - Static method in class net.sf.basedb.util.AnnotationUtil

Get all annotatable parent items for a given item.

getAllAnnotatableParentItems(DbControl, Annotatable, Filter<Annotatable>, AnnotationUtil.Cache) - Static method in class net.sf.basedb.util.AnnotationUtil

Get all annotatable parent items for a given item.

getAllAnnotationTypesWithInheritanceDisabled(DbControl) - Static method in class net.sf.basedb.core.AnnotationType

Load the IDs of all annotation types with the disable inheritance flag set.

getAllCharsets() - Static method in class net.sf.basedb.core.Config

Get a set containing all character sets known to the current java virtual machine.

getAllCharsets(boolean) - Static method in class net.sf.basedb.util.charset.CharsetUtil

Get all charsets that Config.getAllCharsets() returns and optionally include the fallback charsets.

getAllChildren(DbControl, Set<Integer>) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader

getAllColumnMappings() - Method in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter

getAllColumnMappings() - Method in class net.sf.basedb.plugins.PlateFlatFileImporter

getAllColumnMappings() - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

getAllColumnMappings(boolean) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter

getAllColumnMappings(RawDataType) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter

Loads the column mappings if they hasn't been loaded already.

getAllCurrentContexts(boolean, boolean) - Method in class net.sf.basedb.core.SessionControl

Get a list with the current default contexts.

getAllExtended() - Method in class net.sf.basedb.core.data.RawData

getAllItems() - Method in class net.sf.basedb.core.ItemList

Get a query that returns all items that can possibly be members of this list.

getAllMandatory() - Static method in class net.sf.basedb.core.ClonableProperty

Get a list with all mandatory properties that must be cloned.

getAllMembers(DbControl, Set<Integer>) - Static method in class net.sf.basedb.core.User

Load the ID:s of all users that are direct members of the specified groups.

getAllMembers(Session, Collection<Integer>) - Static method in class net.sf.basedb.core.User

getAllObjects() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile

Get a list of all objects defined in this extensions file.

getAllowImmediateExecution() - Method in class net.sf.basedb.core.data.PluginDefinitionData

If the plugin is allowed to be immediately executed or if it must be added to the job queue.

getAllowImmediateExecution() - Method in class net.sf.basedb.core.PluginDefinition

If immediate execution of jobs are allowed or if they always must go through the job queue.

getAllowMultiple() - Method in class net.sf.basedb.core.data.ItemSubtypeFileTypeData

If multiple files of this type are allowed in a file set or not.

getAllowMultiple() - Method in class net.sf.basedb.core.data.PlatformFileTypeData

If multiple files of this type are allowed in a file set or not.

getAllowMultiple() - Method in class net.sf.basedb.core.ItemSubtypeFileType

Check if more than one file of this type is allowed in a file set or not.

getAllowMultiple() - Method in class net.sf.basedb.core.PlatformFileType

Check if more than one file of this type is allowed in a file set or not.

getAllowMultiple() - Method in interface net.sf.basedb.core.UsableDataFileType

A flag indicating if it is allowed to attach multiple files or only a single one of the given type.

getAllParentExtracts(DbControl, OverviewContext, PhysicalBioAssay) - Static method in class net.sf.basedb.util.overview.validator.PhysicalBioAssayValidator

Get all parent extracts that are associated with the given physical bioassay.

getAllPermissions(SharedData) - Method in class net.sf.basedb.core.SessionControl

Same as SessionControl.getAllPermissions(Item, UserData, ItemKeyData, ProjectKeyData)

getAllPermissions(Item, UserData, ItemKeyData, ProjectKeyData) - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring

Return 0.

getAllPermissions(Item, UserData, ItemKeyData, ProjectKeyData) - Method in class net.sf.basedb.core.Job.SignalKeyring

Return 0.

getAllPermissions(Item, UserData, ItemKeyData, ProjectKeyData) - Method in class net.sf.basedb.core.Keyring

getAllPermissions(Item, UserData, ItemKeyData, ProjectKeyData) - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring

Return 0.

getAllPermissions(Item, UserData, ItemKeyData, ProjectKeyData) - Method in class net.sf.basedb.core.SessionControl

Get the combined permissions for an item of the specified type, owned by the specified user and shared with the specified item and project keys.

getAllResults() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults

getAllRoles() - Method in class net.sf.basedb.core.SessionControl

Get the id of all roles where the logged in user is a member.

getAllRules(DbControl, GenericOverview) - Static method in class net.sf.basedb.util.overview.OverviewUtil

Get all static and extension validation rules grouped by relationship.

getAllSamples(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.PushToParentsTransformer

getAllsubcontexts() - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector

getAlwaysGranted() - Method in class net.sf.basedb.core.plugin.Permissions

Get the permissions that the plugin always should be granted, even if the logged in user doesn't have the permissions already.

getAnalyzeTableSql(String, String, String) - Method in interface net.sf.basedb.core.dbengine.DbEngine

Generate SQL to update the index statistics for a table.

getAnalyzeTableSql(String, String, String) - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine

Return null.

getAnalyzeTableSql(String, String, String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine

Generate analyze table <catalog>.<table>.

getAnalyzeTableSql(String, String, String) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine

Generate ANALYZE <schema>.<table>.

getAndSetCurrentContext(SessionControl, Item, String, PageContext, ItemContext) - Static method in class net.sf.basedb.clients.web.Base

Same as: getAndSetCurrentContext(sc, itemType, subContext, pageContext.getRequest(), defaultContext, false).

getAndSetCurrentContext(SessionControl, Item, String, ServletRequest, ItemContext, boolean) - Static method in class net.sf.basedb.clients.web.Base

Get the current context and update it from request information if available.

getAndSetCurrentContext(SessionControl, Item, PageContext, ItemContext) - Static method in class net.sf.basedb.clients.web.Base

Same as: getAndSetCurrentContext(sc, itemType, null, pageContext.getRequest(), defaultContext, false).

getAndSetCurrentContext(SessionControl, Item, PageContext, ItemContext, boolean) - Static method in class net.sf.basedb.clients.web.Base

Same as: getAndSetCurrentContext(sc, itemType, null, pageContext.getRequest(), defaultContext, resetTemporary).

getAndSetReporterContext(SessionControl, PageContext) - Method in class net.sf.basedb.clients.web.ExperimentExplorer

Get and update the current settings for the reporter context.

getAndSetSpotContext(SessionControl, PageContext) - Method in class net.sf.basedb.clients.web.ExperimentExplorer

Get and update the current settings for the spot context.

getAnnotatable() - Method in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper

The annotatable that we are wrapping.

getAnnotatableFromNode(DbControl, Node) - Static method in class net.sf.basedb.util.overview.loader.AnnotationLoader

Get the annotatable item from the node.

getAnnotatableItems() - Static method in class net.sf.basedb.core.Metadata

Get a set containing all Annotatable item types.

getAnnotatableParents() - Method in interface net.sf.basedb.core.Annotatable

Get all parents objects which are annotatable and the logged in user has read permission to.

getAnnotatableParents() - Method in class net.sf.basedb.core.ArrayBatch

Get the array design.

getAnnotatableParents() - Method in class net.sf.basedb.core.ArrayDesign

Get the plates, if any.

getAnnotatableParents() - Method in class net.sf.basedb.core.ArraySlide

Get the array batch.

getAnnotatableParents() - Method in class net.sf.basedb.core.BioAssay

Get the parent bioassay set, all parent bioassays and all parent root raw bioassays.

getAnnotatableParents() - Method in class net.sf.basedb.core.BioAssaySet

Get the parent bioassay set (if any) and the experiment.

getAnnotatableParents() - Method in class net.sf.basedb.core.BioMaterial

Get all child biomaterial items with a subtype that has the ItemSubtype.getPushAnnotations() flag set.

getAnnotatableParents() - Method in class net.sf.basedb.core.BioPlate

Get the freezer.

getAnnotatableParents() - Method in class net.sf.basedb.core.DerivedBioAssay

Get the extract and parent bioassays or physical bioassays.

getAnnotatableParents() - Method in class net.sf.basedb.core.Experiment

Always null.

getAnnotatableParents() - Method in class net.sf.basedb.core.Extract

Get the tag and parent extracts.

getAnnotatableParents() - Method in class net.sf.basedb.core.File

getAnnotatableParents() - Method in class net.sf.basedb.core.FileServer

getAnnotatableParents() - Method in class net.sf.basedb.core.Hardware

getAnnotatableParents() - Method in class net.sf.basedb.core.ItemList

Always returns null

getAnnotatableParents() - Method in class net.sf.basedb.core.Kit

getAnnotatableParents() - Method in class net.sf.basedb.core.MeasuredBioMaterial

Get the biosource or pooled samples and the bioplate the biomaterial is located on.

getAnnotatableParents() - Method in class net.sf.basedb.core.PhysicalBioAssay

Get the extracts and array slide.

getAnnotatableParents() - Method in class net.sf.basedb.core.Plate

Get the parent plates, if any.

getAnnotatableParents() - Method in class net.sf.basedb.core.PluginConfiguration

getAnnotatableParents() - Method in class net.sf.basedb.core.PluginDefinition

getAnnotatableParents() - Method in class net.sf.basedb.core.Project

getAnnotatableParents() - Method in class net.sf.basedb.core.Protocol

getAnnotatableParents() - Method in class net.sf.basedb.core.RawBioAssay

Get the parent derived bioassay and extract, if any.

getAnnotatableParents() - Method in class net.sf.basedb.core.RootRawBioAssay

Get the raw bioassay.

getAnnotatableParents() - Method in class net.sf.basedb.core.Software

getAnnotatableParents() - Method in class net.sf.basedb.core.Tag

getAnnotatableParents() - Method in class net.sf.basedb.core.Well

Get the parent well, if any.

getAnnotatableParents(int, Collection<Extract>) - Method in class net.sf.basedb.core.PhysicalBioAssay

Get the extracts, possible on a specific assay position or only a given set of specific extracts, and the array slide.

getAnnotatableParents(int, Extract) - Method in class net.sf.basedb.core.PhysicalBioAssay

Get the extracts, possible on a specific assay position or only a specific extract, and the array slide.

getAnnotatableParents(Collection<? extends MeasuredBioMaterial>) - Method in class net.sf.basedb.core.MeasuredBioMaterial

Get the annotable parents, possible only a given set of specific parents items.

getAnnotatableParents(DbControl, OverviewContext, Annotatable) - Static method in class net.sf.basedb.util.overview.OverviewUtil

Get all annotatable parent items for the given item.

getAnnotatableParentWrappers(DbControl) - Method in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper

Get all annotatable parents wrapped inside AnnotatableWrapper:s

getAnnotation() - Method in class net.sf.basedb.util.overview.Fix

Get the annotation that needs to be edited for this fix.

getAnnotation(AnnotationType) - Method in class net.sf.basedb.core.AnnotationSet

Get the Annotation object of the specified annotation type.

getAnnotationFormatter(SessionControl, Annotation, Unit) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory

Get a formatter for nice formatting of annotation values, including units.

getAnnotationGroup(short) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary

Get the annotation group for the bioassay with the give data cube column.

getAnnotationGroups() - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary

Get all annotation groups that was found among the bioassays.

getAnnotationId() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

Get the annotation id from the expression.

getAnnotationIdMethods(DbControl) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Get identification methods that are based on annotations.

getAnnotationJoiner(JoinType) - Static method in class net.sf.basedb.core.HqlQueryJoiners

Get an annotation auto joiner.

getAnnotationMessage() - Method in interface net.sf.basedb.core.AnnotatableProxy

A help message that should tell users how the proxied annotations are used.

getAnnotationMessage() - Method in interface net.sf.basedb.core.plugin.AnnotationSetterPlugin

Get a message that explains what the plug-in does with the annotations it has.

getAnnotationMessage() - Method in class net.sf.basedb.core.PluginConfiguration

Get a message explaining what the proxy does with the annotations.

getAnnotationMessage() - Method in class net.sf.basedb.core.PluginDefinition

Get a message explaining what the proxy does with the annotations.

getAnnotationMessage() - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator

getAnnotationMessage() - Method in class net.sf.basedb.plugins.ManualTransformCreator

getAnnotationMessage() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter

getAnnotations() - Method in interface net.sf.basedb.core.data.AnnotatableData

Short-cut to all annotations belonging to this item.

getAnnotations() - Method in class net.sf.basedb.core.data.AnnotatedData

getAnnotations() - Method in class net.sf.basedb.core.data.AnnotationSetData

The annotations in this annotation set.

getAnnotations() - Method in class net.sf.basedb.core.data.AnnotationTypeData

This is the inverse end.

getAnnotations() - Method in class net.sf.basedb.core.data.BioAssayData

getAnnotations() - Method in class net.sf.basedb.core.data.BioAssaySetData

getAnnotations() - Method in class net.sf.basedb.core.data.PluginDefinitionData

getAnnotations() - Method in class net.sf.basedb.core.data.ProjectData

getAnnotations() - Method in class net.sf.basedb.core.data.RootRawBioAssayData

getAnnotations() - Method in class net.sf.basedb.core.data.WellData

getAnnotations() - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot

Get a list with the all annotations in this snapshot.

getAnnotations(Annotation.Source) - Method in class net.sf.basedb.core.AnnotationSet

Get a query returning annotations with the specified source.

getAnnotationSet() - Method in interface net.sf.basedb.core.Annotatable

Get the annotation set containing the annotations for this item.

getAnnotationSet() - Method in class net.sf.basedb.core.AnnotatedItem

getAnnotationSet() - Method in class net.sf.basedb.core.Annotation

Get the annotation set this annotation belongs to.

getAnnotationSet() - Method in class net.sf.basedb.core.BioAssay

getAnnotationSet() - Method in class net.sf.basedb.core.BioAssaySet

getAnnotationSet() - Method in interface net.sf.basedb.core.data.AnnotatableData

Get the annotation set that holds the annotations for an item.

getAnnotationSet() - Method in class net.sf.basedb.core.data.AnnotatedData

getAnnotationSet() - Method in class net.sf.basedb.core.data.AnnotationData

Get the annotation set this annotation primarily belongs to.

getAnnotationSet() - Method in class net.sf.basedb.core.data.BioAssayData

getAnnotationSet() - Method in class net.sf.basedb.core.data.BioAssaySetData

getAnnotationSet() - Method in class net.sf.basedb.core.data.PluginDefinitionData

getAnnotationSet() - Method in class net.sf.basedb.core.data.ProjectData

getAnnotationSet() - Method in class net.sf.basedb.core.data.RootRawBioAssayData

getAnnotationSet() - Method in class net.sf.basedb.core.data.WellData

getAnnotationSet() - Method in class net.sf.basedb.core.PluginDefinition

getAnnotationSet() - Method in class net.sf.basedb.core.Project

getAnnotationSet() - Method in class net.sf.basedb.core.RootRawBioAssay

getAnnotationSet() - Method in class net.sf.basedb.core.Well

getAnnotationSet(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot

Get the annotation set this is a snapshot of.

getAnnotationSetId() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink

getAnnotationSetId() - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot

Get the id of the annotation set this is a snapshot of.

getAnnotationSummary(DbControl, AnnotationType) - Method in class net.sf.basedb.clients.web.ExperimentExplorer

Get an AnnotationSummary object which can be used to calculate means and other values for each annotation group.

getAnnotationType() - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary

Get the annotation type this summary is based on.

getAnnotationType() - Method in class net.sf.basedb.core.Annotation

Get the annotation type of this annotation.

getAnnotationType() - Method in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo

Get the annotation type.

getAnnotationType() - Method in class net.sf.basedb.core.data.AnnotationData

Get the type of this annotation.

getAnnotationType() - Method in class net.sf.basedb.core.query.AnnotationExpression

getAnnotationType() - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil

The annotation type that this loader load annotations from.

getAnnotationType() - Method in class net.sf.basedb.util.annotations.InheritSpecification

getAnnotationType() - Method in class net.sf.basedb.util.export.spotdata.AnnotationAssayField

Get the configured annotation type.

getAnnotationType() - Method in class net.sf.basedb.util.overview.Fix

Get the annotation type of the annotation that needs to be edited for this fix.

getAnnotationType(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

Get the annotation type.

getAnnotationTypeEnum(DbControl, AnnotationType) - Static method in class net.sf.basedb.clients.web.Base

Get an Enumeration that is suitable to use in a column definition for a table for an annotation type.

getAnnotationTypeId() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink

getAnnotationTypeId() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

Get the id of the annotation type.

getAnnotationTypeIds() - Method in class net.sf.basedb.clients.web.ExperimentExplorer

Get the selected annotation types.

getAnnotationTypes() - Method in interface net.sf.basedb.core.AnnotatableProxy

Get the annotation types that can be proxied.

getAnnotationTypes() - Method in class net.sf.basedb.core.data.AnnotationTypeCategoryData

This is the inverse end.

getAnnotationTypes() - Method in interface net.sf.basedb.core.plugin.AnnotationSetterPlugin

Create a query that returns the annotation types that can be used by the current plug-in.

getAnnotationTypes() - Method in class net.sf.basedb.core.PluginConfiguration

Get the annotation types that can be used by this configuration.

getAnnotationTypes() - Method in class net.sf.basedb.core.PluginDefinition

Get the annotation types that can be used by this configuration.

getAnnotationTypes() - Method in class net.sf.basedb.plugins.Base1PluginExecuter

Get the experimental factors connected to a experiment.

getAnnotationTypes() - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator

Return a query that finds annotation types for bioassay sets.

getAnnotationTypes() - Method in class net.sf.basedb.plugins.ManualTransformCreator

Return a query that finds annotation types for bioassay sets.

getAnnotationTypes() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter

Return a query that finds annotation types for raw bioassays.

getAnnotationTypes(DbControl, boolean) - Method in class net.sf.basedb.clients.web.ExperimentExplorer

Get the annotation types that are of interest in this experiment.

getAnnotationTypes(Item) - Method in class net.sf.basedb.core.AnnotationTypeCategory

Gets a query that returns the annotation types that are members of this category

getAnnotationTypesQuery(AnnotatableProxy) - Static method in class net.sf.basedb.clients.web.Base

Get a query that returns all annotation types defined for a AnnotatableProxy item.

getAnnotationTypesQuery(Item) - Static method in class net.sf.basedb.clients.web.Base

Get a query that returns all annotation types defined for a particular item type.

getAnnotationTypesQuery(Item, Boolean) - Static method in class net.sf.basedb.clients.web.Base

Get a query that returns all annotation types defined for a particular item type and, optionally, with a specific protocol parameter setting.

getAnnotationValues() - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup

Get all annotation values in this annotation group.

getAnnotationValues(DbControl, SnapshotManager, BioAssay, AnnotationType) - Static method in class net.sf.basedb.util.BioAssaySetUtil

Find the annotation values for a given annotation type on a bioassay.

getAnyToAny() - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext

Get the current any-to-any link pointing to the file.

getAppId() - Method in class net.sf.basedb.core.data.SchemaVersionData

The ID of the application the schema version is valid for.

getAppId() - Method in class net.sf.basedb.core.hibernate.SessionFactoryConfiguration

Deprecated.

Get the application id for schema versioning.

getAppId() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration

Get the application id for schema versioning.

getApproximateRowCountSql(String, String, String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine

getApproximateRowCountSql(String, String, String) - Method in interface net.sf.basedb.core.dbengine.DbEngine

Get an SQL statement that returns an approximate count for the number of rows in the given table.

getApproximateRowCountSql(String, String, String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine

getApproximateRowCountSql(String, String, String) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine

getApproximateSize() - Method in class net.sf.basedb.core.hibernate.TypeWrapper

Get the number of bytes a single value for this type occupies in a database (approximately).

getArrayBatch() - Method in class net.sf.basedb.core.ArraySlide

Get the ArrayBatch item to which this slide belongs.

getArrayBatch() - Method in class net.sf.basedb.core.data.ArraySlideData

Get the arrayBatch of this slide.

getArrayBatches() - Method in class net.sf.basedb.core.ArrayDesign

Get a query that returns the batches for this design.

getArrayBatches() - Method in class net.sf.basedb.core.data.ArrayDesignData

This is the inverse end.

getArrayDesign() - Method in class net.sf.basedb.core.ArrayBatch

Get the ArrayDesign item that was used for this batch.

getArrayDesign() - Method in class net.sf.basedb.core.ArrayDesignBlock

Get the ArrayDesign that is linked with this block.

getArrayDesign() - Method in class net.sf.basedb.core.ArrayDesignPlate

Gets this item's ArrayDesign.

getArrayDesign() - Method in class net.sf.basedb.core.data.ArrayBatchData

Get the array design item that was used for this batch.

getArrayDesign() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData

Used by Hibernate to link with ArrayDesign.

getArrayDesign() - Method in class net.sf.basedb.core.data.ArrayDesignPlateData

Get the ArrayDesign

getArrayDesign() - Method in class net.sf.basedb.core.data.RawBioAssayData

Get the array design used for the hybridization this raw bio assay comes from.

getArrayDesign() - Method in class net.sf.basedb.core.DerivedBioAssay

Get the array design connected to this derived bioassay by following the path from the physical bioassay to the array slide to the array batch to the array design.

getArrayDesign() - Method in class net.sf.basedb.core.FeatureBatcher

Get the array design this batcher is used for.

getArrayDesign() - Method in class net.sf.basedb.core.RawBioAssay

Get the ArrayDesign this raw data uses.

getArrayDesignBlock() - Method in class net.sf.basedb.core.data.FeatureData

Get the arraydesignblock of this feature.

getArrayDesignBlock(DbControl, FeatureData) - Static method in class net.sf.basedb.core.Feature

Get the array design block from a feature.

getArrayDesignBlocks() - Method in class net.sf.basedb.core.ArrayDesign

Get a query that returns the block of this array design.

getArrayDesignBlocks() - Method in class net.sf.basedb.core.data.ArrayDesignData

This is the inverse end.

getArrayDesignPlates() - Method in class net.sf.basedb.core.ArrayDesign

Get plate connections for this array design.

getArrayDesigns() - Method in class net.sf.basedb.core.data.JobData

This is the inverse end.

getArrayDesigns() - Method in class net.sf.basedb.core.data.PlateData

Used by Hibernate to link with the arraydesign for this plate.

getArraySlide() - Method in class net.sf.basedb.core.data.PhysicalBioAssayData

Get the array slide.

getArraySlide() - Method in class net.sf.basedb.core.PhysicalBioAssay

Get the ArraySlide this hyridization is using.

getArraySlides() - Method in class net.sf.basedb.core.ArrayBatch

Get a query that returns the slides in this batch.

getArraySlides() - Method in class net.sf.basedb.core.data.ArrayBatchData

This is the inverse end.

getAssayAnnotationField(String, String) - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter

Get an assay annotation field.

getAssayAnnotationsWriter() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter

Get the writer were assay annotations should be printed.

getAssayField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.AdvancedFieldConverter

getAssayField(String, boolean) - Method in interface net.sf.basedb.util.export.spotdata.ExportableFieldConverter

Create an assay field for the given name.

getAssayField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.StandardFieldConverter

Find an assay field.

getAssayFields() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

Get the list of registered assay fields, in the order they were registered.

getAssayFields() - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter

getAssayFields() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter

getAssayFields() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo

Get a list with all assay data fields, in the order they appear in the file.

getAssayFields(DbControl, BioAssaySet) - Method in class net.sf.basedb.plugins.BfsExporterPlugin

getAssayIndex(short) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

Get the cached index value for an assay when you know the assay's column number.

getAssayPropertyField(String, String) - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter

Get a static assay property field, such as name, description or id.

getAssays() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo

Get a list with the ID:s of all assays in the section, in the order they appear in the data columns.

getAssaysHaveParentAssaysMapping() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo

A flag that indicates if the BASEfile includes a mapping from child to parent assays.

getAssayValue(DbControl, BioAssay) - Method in class net.sf.basedb.util.export.spotdata.AnnotationAssayField

Return all annotation values that are related to the specified bioassay, or null if not configured.

getAssayValue(DbControl, BioAssay) - Method in interface net.sf.basedb.util.export.spotdata.AssayField

Get the values for the given bioassay.

getAssayValue(DbControl, BioAssay) - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField

Return all values that are given by the specified property.

getAssociatedDataFileType(DataFileType, boolean) - Method in class net.sf.basedb.core.ItemSubtype

Get information about a data file type that has been associated with this item subtype.

getAttribute(String) - Method in class net.sf.basedb.core.authentication.LoginRequest

Get the value of an extra attribute to use for the login request.

getAttribute(String) - Method in class net.sf.basedb.util.extensions.AboutBean

getAttribute(String) - Method in class net.sf.basedb.util.extensions.ClientContext

Get an attribute of the context.

getAttribute(String) - Method in interface net.sf.basedb.util.extensions.ExtendedAbout

Get extra information

getAttribute(String) - Method in class net.sf.basedb.util.extensions.ExtensionContext

getAttribute(String) - Method in class net.sf.basedb.util.extensions.ExtensionPointContext

Always null, since this is an extension point context.

getAttribute(String) - Method in class net.sf.basedb.util.extensions.InvokationContext

Get the value of an attribute that has been registered for the extension.

getAttribute(String) - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout

getAttribute(String, String) - Method in class net.sf.basedb.util.extensions.Registry

Get the value of a extra attribute for a registered extension or extension point.

getAttribute(NodeAttribute<T>) - Method in class net.sf.basedb.util.overview.Node

Get the value for a node attribute.

getAttributeNames() - Method in class net.sf.basedb.util.extensions.AboutBean

getAttributeNames() - Method in interface net.sf.basedb.util.extensions.ExtendedAbout

Get all extra attribute names.

getAttributeNames() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout

getAttributesString(Object) - Static method in class net.sf.basedb.clients.web.extensions.DynamicActionAttributeSupport

If the object implements DynamicActionAttributes interface, get a string with all dynamic attributes, otherwise an empty string.

getAuthenticationMethod() - Method in class net.sf.basedb.core.authentication.AuthenticatedUser

Get the authentication method that was used to verify the login.

getAuthenticationMethod() - Method in class net.sf.basedb.core.data.SessionData

Get the authentication method used for this session.

getAuthenticationMethod() - Method in class net.sf.basedb.core.Session

Get the authentication method that was used to login to this session.

getAuthenticationMethod() - Method in class net.sf.basedb.core.SessionControl

Get the method that was used to authenticate the currently logged in user.

getAuthors() - Method in class net.sf.basedb.core.data.ExperimentData

Get the authors for this experiment.

getAuthors() - Method in class net.sf.basedb.core.Experiment

Get the authors of the publication for this experiment.

getAutoCompress() - Method in class net.sf.basedb.core.data.DirectoryData

If files that are uploaded to this directory be compressed or not.

getAutoCompress() - Method in class net.sf.basedb.core.data.MimeTypeData

If files of this MIME type should use auto-compression or not.

getAutoCompress() - Method in class net.sf.basedb.core.Directory

If files that are uploaded to this directory should be compressed or not.

getAutoCompress() - Method in class net.sf.basedb.core.MimeType

If files of this MIME type should automatically be compressed when they are uploaded to BASE.

getAutoFormatter() - Method in class net.sf.basedb.util.excel.XlsxTableWriter

Get the auto-formatter instance to use for columns that has no specified formatter via TableWriter.setColumnFormatter(int, Formatter).

getAutoJoinType() - Method in class net.sf.basedb.core.query.ReporterListExpression

Get the join type for automatic joins.

getAutoPermission() - Method in class net.sf.basedb.core.data.ProjectData

The permissions to use with automatic sharing to this project.

getAutoPermission() - Method in class net.sf.basedb.core.Project

The permissions to use when automatically sharing new items to the project when it is the active project.

getAutoShare() - Method in class net.sf.basedb.core.data.DirectoryData

If new files and subdirectories should inherit the share permission on this directory or not.

getAutoShare() - Method in class net.sf.basedb.core.Directory

If new files and subdirectories that are created in this directory automatically should be shared wtih the same permissions as this directory.

getAverageExpression(Expression) - Method in enum class net.sf.basedb.core.Formula.AverageMethod

Given an expression, create an expression that takes the correct average of it.

getAverageMethod() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn

getAverageMethod() - Method in class net.sf.basedb.core.data.ExtraValueTypeData

The average method for thid formula: 0 = none, Formula.AverageMethod.NONE; no average is defined for this formula 1 = geometric mean, Formula.AverageMethod.GEOMETRIC_MEAN; this formula uses geometric mean 2 = arithmetic mean, Formula.AverageMethod.ARITHMETIC_MEAN; this formula uses arithmetic mean 3 = min, Formula.AverageMethod.MIN; this formula uses the min value as a "mean" 4 = max, Formula.AverageMethod.MAX; this formula uses the max value as a "mean"

getAverageMethod() - Method in class net.sf.basedb.core.data.FormulaData

The average method for thid formula: 0 = none, Formula.AverageMethod.NONE; no average is defined for this formula 1 = geometric mean, Formula.AverageMethod.GEOMETRIC_MEAN; this formula uses geometric mean 2 = arithmetic mean, Formula.AverageMethod.ARITHMETIC_MEAN; this formula uses arithmetic mean 3 = min, Formula.AverageMethod.MIN; this formula uses the min value as a "mean" 4 = max, Formula.AverageMethod.MAX; this formula uses the max value as a "mean"

getAverageMethod() - Method in class net.sf.basedb.core.data.ReporterClonePropertyData

The code for the averate method to use when calculating averages.

getAverageMethod() - Method in class net.sf.basedb.core.ExtendedProperty

Which method to use when calculating the average of a set of values.

getAverageMethod() - Method in class net.sf.basedb.core.ExtraValueType

Get the average method for this extra value type.

getAverageMethod() - Method in class net.sf.basedb.core.Formula

Get the average method for this formula.

getAverageMethod() - Method in enum class net.sf.basedb.core.IntensityTransform

Get the averaging method to use when averaging values that has been transformed with the specified transformation.

getAverageMethod() - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField

Get the average method to use if the exporter is exporting averaged data.

getAverageMethod() - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField

Get the average method to use if the exporter is exporting averaged data.

getAverageOnReporter() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

getAverageOnReporter() - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter

getAvg() - Method in class net.sf.basedb.core.query.GeometricMeanExpression

getAwtColor() - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup

Get the AWT color object that corresponds to the HTML color string.

getBarcode() - Method in class net.sf.basedb.core.ArraySlide

Get the barcode of the slide.

getBarcode() - Method in class net.sf.basedb.core.BioPlate

Gets the barcode of this bio plate.

getBarcode() - Method in class net.sf.basedb.core.data.ArraySlideData

Get the barcode of the slide.

getBarcode() - Method in class net.sf.basedb.core.data.BioPlateData

Get the barcode for the bioplate.

getBarcode() - Method in class net.sf.basedb.core.data.PlateData

Get the barcode for the plate.

getBarcode() - Method in class net.sf.basedb.core.Plate

Get the barcode of this plate.

getBaseFileParser() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter

Get the underlying parser for the BASEfile.

getBaseFileWriter() - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter

Get the writer that writes the data to the file.

getBaseStyle() - Method in class net.sf.basedb.util.excel.CellStyleCreator

Get the current base style for new cells.

getBaseVersion() - Method in class net.sf.basedb.clients.web.taglib.Page

getBasicData() - Method in class net.sf.basedb.core.BasicItem

getBatchIndex() - Method in class net.sf.basedb.core.ArraySlide

Get the index of this slide in the batch.

getBatchIndex() - Method in class net.sf.basedb.core.data.ArraySlideData

Get the index of this slide in the batch.

getBatchSize() - Method in class net.sf.basedb.core.AbstractBatcher

getBatchSize() - Method in interface net.sf.basedb.core.Batcher

Get the current batch size of the batcher.

getBestMatch(String, Collection<? extends String>) - Method in class net.sf.basedb.util.fuzzy.StringMatcher

Find the string that is most similar to a given string in a list of strings.

getBestPairs(Collection<? extends String>, Collection<? extends String>) - Method in class net.sf.basedb.util.fuzzy.StringMatcher

Match strings in two lists.

getBFSSubtype() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter

Get the BFS subtype.

getBFSSubtype() - Method in class net.sf.basedb.util.export.spotdata.MatrixBfsExporter

getBFSSubtype() - Method in class net.sf.basedb.util.export.spotdata.SerialBfsExporter

getBin(int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramSeries

getBioAssay(DbControl, short) - Method in class net.sf.basedb.clients.web.ExperimentExplorer

Get the bioassay with the specified column number in the data cube.

getBioAssays() - Method in class net.sf.basedb.core.BioAssaySet

Get a query returning the bioassays that are part of this bioassayset.

getBioAssays() - Method in class net.sf.basedb.core.data.BioAssaySetData

This is the inverse end.

getBioAssays() - Method in class net.sf.basedb.core.data.RawBioAssayData

This is the inverse end.

getBioAssays() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

Get a list with all bioassays in the source bioassay set.

getBioAssaySet() - Method in class net.sf.basedb.core.BioAssay

Get the bioassayset this bioassay belongs to.

getBioAssaySet() - Method in class net.sf.basedb.core.data.BioAssayData

Get the bioassayset this bioassay belongs to.

getBioAssaySet() - Method in class net.sf.basedb.core.data.ExtraValueData

Get the bioassayset this extra value belongs to.

getBioAssaySet() - Method in class net.sf.basedb.core.ExtraValue

Get the bioassayset this extra value belongs to.

getBioAssaySet(DbControl) - Method in class net.sf.basedb.clients.web.ExperimentExplorer

Get the bioassay set that is currently beeing explored.

getBioAssaySets() - Method in class net.sf.basedb.core.data.ExperimentData

This is the inverse end.

getBioAssaySets() - Method in class net.sf.basedb.core.Experiment

Get a query that return all bioassaysets in this experiment.

getBioMaterial() - Method in class net.sf.basedb.core.BioMaterialEvent

Get the MeasuredBioMaterial that was affected or created by this event.

getBioMaterial() - Method in class net.sf.basedb.core.BioMaterialEventSource

Get the biomaterial that was used as a source in this event.

getBioMaterial() - Method in class net.sf.basedb.core.BioWell

Gets the MeasuredBioMaterial connected to this biowell.

getBioMaterial() - Method in class net.sf.basedb.core.data.BioMaterialEventData

Get the biomaterial produced or affected by this event.

getBioMaterial() - Method in class net.sf.basedb.core.data.BioMaterialEventSourceData

Get the parent biomaterial that was used in the event.

getBioMaterial() - Method in class net.sf.basedb.core.data.BioWellData

The MeasuredBioMaterialData used in this well.

getBioMaterial(PlateCoordinate) - Method in class net.sf.basedb.core.BioPlate

Get the biomaterial in the well at the given location.

getBioMaterialEvents() - Method in class net.sf.basedb.core.BioPlateEvent

Get a query returning all biomaterial events linked to this event.

getBioMaterialEvents() - Method in class net.sf.basedb.core.data.BioPlateEventParticipantData

This is the inverse end.

getBioMaterialType() - Method in class net.sf.basedb.core.BioPlateType

Get the biomaterial type that can be stored on plates of this type.

getBioMaterialType() - Method in class net.sf.basedb.core.BioWell

Get the type of biomaterial that is placed in this well.

getBioMaterialType() - Method in class net.sf.basedb.core.data.BioPlateTypeData

If set, plates using this type can only hold the specific biomaterial type (eg. samples, extracts or labeled extracts).

getBioPlate() - Method in class net.sf.basedb.core.BioPlateEventParticipant

Get the BioPlate.

getBioPlate() - Method in class net.sf.basedb.core.data.BioPlateEventParticipantData

The bioplate that is participating in the event.

getBioPlate() - Method in class net.sf.basedb.core.data.BioWellData

The bioplate this well belongs to.

getBioPlateEventParticipant() - Method in class net.sf.basedb.core.BioMaterialEvent

Get the bioplate event participant that is the master of this event.

getBioPlateEventParticipant() - Method in class net.sf.basedb.core.data.BioMaterialEventData

Get the bioplate event that is the master event for this event.

getBioPlates() - Method in class net.sf.basedb.core.BioPlateType

Creates a query that returns all bioplates that are using this type.

getBioPlates() - Method in class net.sf.basedb.core.data.BioPlateTypeData

The bioplates that use this type.

getBioPlateType() - Method in class net.sf.basedb.core.BioPlate

Get the BioPlateType of this bioplate.

getBioPlateType() - Method in class net.sf.basedb.core.data.BioPlateData

Get the type of the bioplate.

getBioWell() - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData

Get the bio well.

getBioWell() - Method in class net.sf.basedb.core.MeasuredBioMaterial

Get the well this biomaterial is located in.

getBioWell(int, int) - Method in class net.sf.basedb.core.BioPlate

Gets bio well for specific location.

getBioWell(PlateCoordinate) - Method in class net.sf.basedb.core.BioPlate

Gets bio well for specific location.

getBioWells() - Method in class net.sf.basedb.core.BioPlate

Gets a query that returns all BioWells on this plate.

getBioWells() - Method in class net.sf.basedb.core.data.BioPlateData

The wells on this plate.

getBlock() - Method in class net.sf.basedb.core.BlockInfo

Get the block number.

getBlock() - Method in class net.sf.basedb.core.data.RawData

getBlock() - Method in class net.sf.basedb.core.FeatureCoordinate

getBlock() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock

getBlockNumber() - Method in class net.sf.basedb.core.ArrayDesignBlock

Get the block number of this block.

getBlockNumber() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData

Get the block number of this block.

getBlockNumber() - Method in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section

getBlockSizeX() - Method in class net.sf.basedb.core.ArrayDesignBlock

Get the number of columns in this block.

getBlockSizeX() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData

Get the maximum number of rows in this block.

getBlockSizeX() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock

getBlockSizeY() - Method in class net.sf.basedb.core.ArrayDesignBlock

Get the number of rows in this block.

getBlockSizeY() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData

Get the maximum number of columns in this block.

getBlockSizeY() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock

getBofType() - Method in class net.sf.basedb.util.parser.FlatFileParser

Get the value captured by the BOF marker regular expression.

getBoolean(String) - Static method in class net.sf.basedb.core.Config

Get the configuration setting specified by key as a boolean value.

getBoolean(String) - Method in class net.sf.basedb.plugins.Base1PluginExecuter

Creates a boolean from a string.

getBoolean(String) - Static method in class net.sf.basedb.util.Values

Convert a string to a boolean. '0', 'no', 'false', '' and the null string are converted to FALSE, all other values are converted to TRUE.

getBoolean(String, boolean) - Static method in class net.sf.basedb.util.Values

Convert a string to a boolean.

getBooleanAttribute(Element, String, boolean) - Static method in class net.sf.basedb.util.XmlUtil2

Get the value of an attribute as a boolean.

getBooleanFormatParameter() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport

getBooleanFormatter(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory

Get the logged in user's formatter for boolean values.

getBooleanOption(String, boolean) - Method in class net.sf.basedb.core.AnnotationType

Get an option and convert the value to a boolean.

getBooleanValues() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink

getBuild() - Static method in class net.sf.basedb.core.Application

Get the build number.

getBuild() - Method in class net.sf.basedb.core.data.SchemaVersionData

The build number.

getBuild() - Static method in class net.sf.basedb.core.Version

Get the build version.

getButtonclass() - Method in class net.sf.basedb.clients.web.taglib.Select

getButtonicon() - Method in class net.sf.basedb.clients.web.taglib.Select

getButtonstyle() - Method in class net.sf.basedb.clients.web.taglib.Select

getButtonTag() - Method in class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRenderer

Get the HTML tag to use for the "button".

getButtonTag() - Method in class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRendererFactory

Get the HTML tag to use for the "button".

getButtontitle() - Method in class net.sf.basedb.clients.web.taglib.Select

getByClassName(DbControl, String) - Static method in class net.sf.basedb.core.PluginDefinition

Get a PluginDefinition item when you know the class name.

getByExtension(DbControl, String) - Static method in class net.sf.basedb.core.MimeType

Get a MimeType item when you know the file extension.

getByExternalId(String) - Method in class net.sf.basedb.core.ReporterBatcher

Get a reporter when you know the external id.

getByExternalId(String, boolean) - Method in class net.sf.basedb.core.ReporterBatcher

Get a reporter when you know the external id.

getByExternalId(DbControl, String) - Static method in class net.sf.basedb.core.Client

Get a Client item when you know the external ID.

getByExternalId(DbControl, String) - Static method in class net.sf.basedb.core.DataFileType

Get a DataFileType item when you know the external ID.

getByExternalId(DbControl, String) - Static method in class net.sf.basedb.core.ExtraValueType

Get a ExtraValueType when you know the external id.

getByExternalId(DbControl, String) - Static method in class net.sf.basedb.core.JobAgent

Get a JobAgent item when you know the external ID.

getByExternalId(DbControl, String) - Static method in class net.sf.basedb.core.Platform

Get a Platform item when you know the external ID.

getByExternalId(DbControl, String) - Static method in class net.sf.basedb.core.PlatformVariant

Get a PlatformVariant item when you know the external ID.

getByExternalId(DbControl, String) - Static method in class net.sf.basedb.core.Reporter

Get a ReporterData object when you know the external id.

getByExternalId(DbControl, String, Experiment) - Static method in class net.sf.basedb.core.Reporter

Get a ReporterData object when you know the external id, possibly using the cloned reporter annotations of the given experiment.

getById - Variable in enum class net.sf.basedb.core.Item

getById(DbControl, int) - Static method in class net.sf.basedb.core.Annotation

Get an Annotation item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.AnnotationSet

Get an AnnotationSet item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.AnnotationType

Get an AnnotationType item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.AnnotationTypeCategory

Get an AnnotationTypeCategory item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.AnyToAny

Get an AnyToAny link when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.ArrayBatch

Get a ArrayBatch object when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.ArrayDesign

Get an ArrayDesign item when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.ArrayDesignBlock

Get a ArrayDesignBlock object when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.ArrayDesignPlate

Get a ArrayDesignPlate item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.ArraySlide

Get a ArraySlide object when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.BioAssay

Get a BioAssay item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.BioAssaySet

Get a BioAssaySet item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.BioMaterial

Get a biomaterial item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.BioMaterialEvent

Get a BioMaterialEvent item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.BioPlate

Gets a BioPlate when knowing the item's id

getById(DbControl, int) - Static method in class net.sf.basedb.core.BioPlateEvent

Get a BioPlateEvent item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.BioPlateEventParticipant

Get a BioPlateEventParticipant item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.BioPlateEventType

Gets a BioPlate event type when knowing the item's id

getById(DbControl, int) - Static method in class net.sf.basedb.core.BioPlateType

Gets a BioPlate type when knowing the item's id

getById(DbControl, int) - Static method in class net.sf.basedb.core.BioSource

Get an BioSource item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.BioWell

Get a BioWell item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.ChangeHistory

Get a ChangeHistory item when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.Client

Get a Client item when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.ClientDefaultSetting

Get a ClientDefaultSetting item when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.DataCube

Get a VirtualDb item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.DataCubeColumn

Get a DataCubeColumn item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.DataCubeExtraValue

Get a DataCubeExtraValue item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.DataCubeFilter

Get a DataCubeFilter item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.DataCubeLayer

Get a DataCubeLayer item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.DataFileType

Get a DataFileType object when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.DerivedBioAssay

Get a DerivedBioAssay item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.Directory

Get a Directory item when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.Experiment

Get an Experiment item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.Extract

Get an Extract item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.ExtraValue

Get an ExtraValue item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.ExtraValueType

Get an ExtraValueType object when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.File

Get a File item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.FileServer

Get a FileServer item when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.FileSet

Get a FileSet item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.FileSetMember

Get a FileSetMember object when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.Formula

Get a Formula item when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.GlobalDefaultSetting

Get a ClientDefaultSetting item when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.Group

Get a Group item when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.Hardware

Get a Hardware item when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.Help

Get a Help item when you know the ID.

getById(DbControl, int) - Method in enum class net.sf.basedb.core.Item

Get the item of the type represented by this enumeration constant with the specified id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.ItemKey

Get an ItemKey item when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.ItemList

Get an ItemList item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.ItemSubtype

Get an item subtype object when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.ItemSubtypeFileType

Get a PlatformFileType object when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.Job

Get a Job item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.JobAgent

Get a JobAgent object when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.JobAgentSettings

Get a JobAgentSettings item when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.Kit

Get a Kit item when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.Message

Get a Message item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.MimeType

Get a MimeType object when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.News

Get a News item when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.PermissionTemplate

Get a permission template item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.PhysicalBioAssay

Get a Hybridization item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.Plate

Get a Plate item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.PlateEvent

Get a PlateEvent item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.PlateEventType

Get a PlateEventType item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.PlateGeometry

Get a PlateGeometry item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.PlateMapping

Get a PlateMapping item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.PlateType

Get a PlateType item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.Platform

Get a Platform object when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.PlatformFileType

Get a PlatformFileType object when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.PlatformVariant

Get a PlatformVariant object when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.PluginConfiguration

Get a PluginConfiguration item when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.PluginDefinition

Get a PluginDefinition item when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.PluginType

Get a PluginType object when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.Project

Get a Project item when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.ProjectKey

Get a ProjectKey item when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.Protocol

Get a Protocol item when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.Quantity

Get a Quantity object when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.Quota

Get a Quota item when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.QuotaType

Get a QuotaType object when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.RawBioAssay

Get a RawBioAssay object when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.Reporter

Get a ReporterData object when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.ReporterCloneTemplate

Get a reporter clone template item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.ReporterList

Get a ReporterList item when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.ReporterType

Get a ReporterType object when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.Role

Get a Role item when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.RoleKey

Get a RoleKey item when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.RootRawBioAssay

Get a RootRawBioAssay item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.Sample

Get an Sample item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.Session

Get a Session item when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.Setting

Get a Setting item when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.Software

Get a Software item when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.SyncFilter

Get a SyncFilter item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.Tag

Get a Tag item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.Transformation

Get a Transformation item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.Unit

Get a Unit object when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.User

Get a User item when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.UserClientSetting

Get a UserClientSetting item when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.UserDefaultSetting

Get a UserDefaultSetting item when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.UserDevice

Get a UserDevice item when you know the ID.

getById(DbControl, int) - Static method in class net.sf.basedb.core.VirtualDb

Get a VirtualDb item when you know the id.

getById(DbControl, int) - Static method in class net.sf.basedb.core.Well

Get a Well item when you know the id.

getById(DbControl, int, boolean) - Static method in class net.sf.basedb.core.Annotation

Get an Annotation item when you know the id and ignore the rules for project-specific annotations when modifying the values.

getById(DbControl, int, Experiment) - Static method in class net.sf.basedb.core.Reporter

Get a ReporterData object when you know the ID, possibly using the cloned reporter annotations of the given experiment.

getById(DbControl, String) - Static method in class net.sf.basedb.core.BioPlateEventType

Gets a BioPlate event type when knowing the item's system id

getByInterfaceName(DbControl, String) - Static method in class net.sf.basedb.core.PluginType

Get a PluginType object when you know the interface name it represents.

getByItemType(DbControl, Item) - Static method in class net.sf.basedb.core.RoleKey

Get a RoleKey item when you know the Item type.

getByName(String) - Static method in enum class net.sf.basedb.util.formatter.BooleanFormatter.Type

Get the type by name of the static constant defined in this class.

getByName(DbControl, BasicItem, String) - Static method in class net.sf.basedb.core.AnyToAny

Get an AnyToAny link when you know the item it is linking from and the name of the link.

getByPath(DbControl, Path) - Static method in class net.sf.basedb.core.Directory

Get a Directory item when you know the path.

getByPath(DbControl, Path, boolean) - Static method in class net.sf.basedb.core.Directory

Get an existing Directory or create a new one if the given path doesn't exists.

getByPath(DbControl, Path, boolean) - Static method in class net.sf.basedb.core.File

Get a File item when you know the path.

getBytes() - Method in class net.sf.basedb.core.data.DataCubeData

The number of bytes the analysed data in this cube occupies on disk.

getBytes() - Method in class net.sf.basedb.core.data.DataCubeExtraValueData

The number of bytes the extra values data occupies on disk.

getBytes() - Method in class net.sf.basedb.core.data.DataCubeFilterData

The number of bytes the analysed data in this cube occupies on disk.

getBytes() - Method in class net.sf.basedb.core.data.DataCubeLayerData

The number of bytes the analysed data in this cube occupies on disk.

getBytes() - Method in class net.sf.basedb.core.data.DiskUsageData

Get the number of bytes the DiskConsumable item is using.

getBytes() - Method in class net.sf.basedb.core.data.ExperimentData

The number of bytes the analysed data in this experiment occupies on disk.

getBytes() - Method in class net.sf.basedb.core.data.RawBioAssayData

The number of bytes the raw data occupies on disk.

getBytes() - Method in class net.sf.basedb.core.data.ReporterCloneTemplateData

The number of bytes the cloned reporter information uses in the dynamic database.

getBytes() - Method in class net.sf.basedb.core.DataCube

Gets the number of bytes the analysed data in this cube occupies on disk.

getBytes() - Method in class net.sf.basedb.core.DataCubeExtraValue

Get the number of bytes the data stored in this layer occupies on disk.

getBytes() - Method in class net.sf.basedb.core.DataCubeFilter

Get the number of bytes the data stored in this filter occupies on disk.

getBytes() - Method in class net.sf.basedb.core.DataCubeLayer

Get the number of bytes the data stored in this layer occupies on disk.

getBytes() - Method in interface net.sf.basedb.core.DiskConsumable

Get the absolute number of bytes this item uses.

getBytes() - Method in class net.sf.basedb.core.DiskUsage

Get the number of bytes the DiskConsumable item is using.

getBytes() - Method in class net.sf.basedb.core.Experiment

getBytes() - Method in class net.sf.basedb.core.File

getBytes() - Method in class net.sf.basedb.core.RawBioAssay

getBytes() - Method in class net.sf.basedb.core.ReporterCloneTemplate

Get the number of bytes the cloned reporter information use in the database.

getBytesPerRow(Experiment) - Method in enum class net.sf.basedb.core.VirtualTable

getBytesPerRow(VirtualDb) - Method in enum class net.sf.basedb.core.VirtualTable

Get the number of bytes a single row in the database occupies.

getByType(FlatFileParser.Data, Type) - Method in interface net.sf.basedb.util.parser.Mapper

getCache() - Method in class net.sf.basedb.util.listable.TransformContext

Get a cache that can be used for storing transformation results for some time.

getCachedDownloadStream() - Method in class net.sf.basedb.core.File

Get a (possible) cached stream for reading from the file.

getCachedObject(Object) - Method in class net.sf.basedb.util.overview.GenericOverview

Retreive an object stored in the overview cache.

getCachedObject(Object) - Method in interface net.sf.basedb.util.overview.OverviewContext

Retreive an object stored in the overview cache.

getCachedQuery(String) - Method in class net.sf.basedb.core.hibernate.AbstractQueryCache

Get a cached query.

getCachedQuery(String, Class<T>) - Method in class net.sf.basedb.core.hibernate.AbstractQueryCache

getCacheKey(int) - Static method in class net.sf.basedb.core.snapshot.SnapshotManager

The static cache key under which the snapshot for the annotation set with the given id is cached.

getCacheMode() - Method in class net.sf.basedb.core.hibernate.QueryWrapper

getCacheMode() - Method in class net.sf.basedb.core.hibernate.SessionWrapper

getCacheRegion() - Method in class net.sf.basedb.core.hibernate.QueryWrapper

getCacheSize() - Method in class net.sf.basedb.clients.web.ExperimentExplorer

The number of reporter id'd to cache.

getCaseSensitiveVarchar(int) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine

Return null.

getCaseSensitiveVarchar(int) - Method in interface net.sf.basedb.core.dbengine.DbEngine

Generate a column declaration that creates a case-sensitive variable-length string column type.

getCaseSensitiveVarchar(int) - Method in class net.sf.basedb.core.dbengine.MySQLEngine

Return varchar(length) CHARACTER SET utf8 COLLATE utf8_bin.

getCatalog() - Method in class net.sf.basedb.core.ServiceSessionControl

getCatalogName(String, String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine

Return the catalog name.

getCatalogName(String, String) - Method in interface net.sf.basedb.core.dbengine.DbEngine

Get the catalog name to use for referencing the given catalog/schema pair.

getCatalogName(String, String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine

Generates a catalog name by combining the catalog and schema name (catalog_schema).

getCategories() - Method in class net.sf.basedb.core.AnnotationType

Get a query that returns the categories an annotation type belongs to.

getCategories() - Method in class net.sf.basedb.core.data.AnnotationTypeData

Get the set that manages the categories of this annotation type.

getCategories() - Method in class net.sf.basedb.core.ItemSubtype

Get a query returning the annotation type categories that are related to this subtype (sub-categories are not checked).

getCategories(List<?>) - Method in class net.sf.basedb.core.ItemSubtype

Get a query returning the annotation type categories that are related to this subtype and associated with the given subcategories.

getCell(int, int) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo

Get the cell at the specified row and column.

getCellClass() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

getCellClass() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction

Optional extra classes to add to table cell (td) tags for this column.

getCellStyle() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

getCellStyle() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction

Optional extra style definition to add to table cell (td) tags for this column.

getCellStyle(String) - Method in class net.sf.basedb.util.excel.CellStyleCreator

Get the cell style for the given format string.

getCellStyleCreator() - Method in class net.sf.basedb.util.excel.XlsxTableWriter

Get the style creator that can be used for custom styling of cells.

getCellValueAsDate(Cell, Formatter<Date>, boolean) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo

Get the cell value as a date.

getCellValueAsNumber(Cell, NumberFormat, boolean) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo

Get the cell value as a number.

getCellValueAsString(Cell) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo

Get the the cell value as a string.

getCertificate(InputStream, String, String) - Static method in class net.sf.basedb.util.ssl.SSLUtil2

Get the certificate that is found in the given input stream.

getCertificateChain(String) - Method in class net.sf.basedb.util.ssl.StaticKeyManager

getChangeHistory() - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData

Get the main history entry the details belong to.

getChangeInfo() - Method in class net.sf.basedb.core.ChangeHistory

Get some additional free-text information about the change.

getChangeInfo() - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData

Get more information about this change.

getChangesBy(Job) - Static method in class net.sf.basedb.core.ChangeHistory

Get all changes made by the specified job.

getChangesBy(User) - Static method in class net.sf.basedb.core.ChangeHistory

Get all changes made by the specified user.

getChangesIn(Session) - Static method in class net.sf.basedb.core.ChangeHistory

Get all changes made in the specified session.

getChangeType() - Method in class net.sf.basedb.core.ChangeHistory

Get the type of change that was made.

getChangeType() - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData

The type of the change: 1 = create, 2 = update, 3 = delete

getChangeType() - Method in class net.sf.basedb.core.log.EntityDetails

Was it a creation/update/deletion?

getChangeType() - Method in class net.sf.basedb.core.log.ManualLogEntry

Get the change type.

getChannel() - Method in class net.sf.basedb.core.RawDataProperty

Get the channel this property belongs to.

getChannels() - Method in class net.sf.basedb.core.data.FormulaData

The number of required channels in the experiment to use this formula, or 0 if the number of channels doesn't matter.

getChannels() - Method in class net.sf.basedb.core.data.PlatformData

The number of channels this platform uses.

getChannels() - Method in class net.sf.basedb.core.data.PlatformVariantData

The number of channels this platform variant uses.

getChannels() - Method in class net.sf.basedb.core.Formula

Get the number of channels required to be able to use this formula.

getChannels() - Method in class net.sf.basedb.core.RawDataType

The number of channels in this raw data type.

getCharacterSet() - Method in class net.sf.basedb.core.data.FileData

Get the character set used in this file (for text-files only).

getCharacterSet() - Method in class net.sf.basedb.core.File

Get the character set used in this file (for text-files only).

getCharacterSet() - Method in class net.sf.basedb.core.plugin.ImportInputStream

Get the character set used by the source if it is a text-file.

getCharacterSet() - Method in class net.sf.basedb.util.FileImportInputStream

Calls File.getCharacterSet(), unless a character set was specified in the constructor.

getCharacterSet() - Method in class net.sf.basedb.util.importer.BaseFileWrapper

getCharacterSet() - Method in class net.sf.basedb.util.importer.DiskFileWrapper

getCharacterSet() - Method in interface net.sf.basedb.util.importer.FileWrapper

Get the character set used in the file.

getCharacterSet() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo

Get the character set used by the file, or null if not known.

getCharacterSet() - Method in class net.sf.basedb.util.uri.UriMetadata

Get the character set used by the resource.

getCharset() - Static method in class net.sf.basedb.core.Config

Get the default character set to use when no other has been specified.

getCharset() - Method in class net.sf.basedb.core.File.CharsetTesterThread

getCharset() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

Get the character set the file uses.

getCharset() - Method in class net.sf.basedb.util.charset.CharsetDetector

Get the character set this detector is configured to use.

getCharset() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil

Get the current character set.

getCharset(String) - Static method in class net.sf.basedb.util.charset.CharsetUtil

Get a character set by name.

getCharset(Request) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

Get the character set the file uses.

getChart() - Method in class net.sf.basedb.util.plot.HistogramPlot

Get the underlying JFreeChar object.

getChart() - Method in class net.sf.basedb.util.plot.ScatterPlot

Get the underlying JFreeChar object.

getChild() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay

Get the real child bioassay object once it has been created and scheduled for saving into the database.

getChild(String) - Method in class net.sf.basedb.util.overview.Node

Get the child node with a specific name.

getChildAssay(int) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo

Get the child bioassay with the given id (from the BASEfile).

getChildAssays() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo

Get information about all child bioassays referenced in the file.

getChildColumns(short) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo

Get all child columns that have been mapped to the specified parent column.

getChildCreationEvents() - Method in class net.sf.basedb.core.BioMaterial

Get a query returning all events where this biomaterial has been used as a source item.

getChildCreationEvents() - Method in class net.sf.basedb.core.data.BioMaterialData

This is the inverse end.

getChildDescriptionParameter(String, String, String) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

Create a plugin parameter that asks for the description of the child bioassay set.

getChildErrors() - Method in class net.sf.basedb.util.overview.Node

Get the number of errors to children of this node.

getChildExtracts() - Method in class net.sf.basedb.core.Extract

Creates a query that returns all child (pooled) extracts that has this extracts as one of it's sources.

getChildHasDifferentReporterPositionMapping() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo

A flag that indicates if the child data has a different position/reporter mapping than the parent bioassay set.

getChildId() - Method in class net.sf.basedb.core.data.keyring.GroupGroups

Get the id of the child group.

getChildNameParameter(String, String, String) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

Create a plugin parameter that asks for the name of the child bioassay set.

getChildNodeDirection() - Method in class net.sf.basedb.util.overview.Node

Get the direction to use when loading children of this node.

getChildPlates() - Method in class net.sf.basedb.core.Plate

Get a query returning the child plates of this plate.

getChildren() - Method in class net.sf.basedb.clients.web.ExperimentExplorer.InExpression

getChildren() - Method in class net.sf.basedb.core.AnnotationRestriction

getChildren() - Method in class net.sf.basedb.core.AnnotationSet.ProjectSpecificAnnotationsRestriction

getChildren() - Method in class net.sf.basedb.core.data.BioAssayData

This is the inverse end to BioAssayData.getParents().

getChildren() - Method in class net.sf.basedb.core.data.BioMaterialData

This is the inverse end.

getChildren() - Method in class net.sf.basedb.core.data.DerivedBioAssayData

This is the inverse end.

getChildren() - Method in class net.sf.basedb.core.data.GroupData

Get the set that manages which other groups are members of this group.

getChildren() - Method in class net.sf.basedb.core.data.PlateData

The childs plates created by plate mappings.

getChildren() - Method in class net.sf.basedb.core.DerivedBioAssay

Get all child derived bioassays.

getChildren() - Method in class net.sf.basedb.core.DynamicJoin

getChildren() - Method in class net.sf.basedb.core.DynamicRestriction

getChildren() - Method in class net.sf.basedb.core.ExtraValueExpression

getChildren() - Method in class net.sf.basedb.core.ExtraValueJoin

getChildren() - Method in class net.sf.basedb.core.MeanRawDataPropertyExpression

getChildren() - Method in class net.sf.basedb.core.query.AbsExpression

getChildren() - Method in class net.sf.basedb.core.query.AddExpression

getChildren() - Method in class net.sf.basedb.core.query.AndRestriction

getChildren() - Method in class net.sf.basedb.core.query.AnnotationJoin

getChildren() - Method in class net.sf.basedb.core.query.AnyToAnyRestriction

getChildren() - Method in class net.sf.basedb.core.query.AscOrder

getChildren() - Method in class net.sf.basedb.core.query.BetweenRestriction

getChildren() - Method in class net.sf.basedb.core.query.BooleanExpression

getChildren() - Method in class net.sf.basedb.core.query.CaseExpression

getChildren() - Method in class net.sf.basedb.core.query.ConditionalQueryElement

getChildren() - Method in class net.sf.basedb.core.query.CountExpression

getChildren() - Method in class net.sf.basedb.core.query.DescOrder

getChildren() - Method in class net.sf.basedb.core.query.DivideExpression

getChildren() - Method in class net.sf.basedb.core.query.EqRestriction

getChildren() - Method in class net.sf.basedb.core.query.ExpExpression

getChildren() - Method in class net.sf.basedb.core.query.ExpressionSelect

getChildren() - Method in class net.sf.basedb.core.query.FloatExpression

getChildren() - Method in class net.sf.basedb.core.query.GeometricMeanExpression

getChildren() - Method in class net.sf.basedb.core.query.GteqRestriction

getChildren() - Method in class net.sf.basedb.core.query.GtRestriction

getChildren() - Method in class net.sf.basedb.core.query.HqlElementsExpression

getChildren() - Method in class net.sf.basedb.core.query.HqlEntityExpression

getChildren() - Method in class net.sf.basedb.core.query.HqlEntityParameterExpression

getChildren() - Method in class net.sf.basedb.core.query.HqlExpression

getChildren() - Method in class net.sf.basedb.core.query.HqlIndexExpression

getChildren() - Method in class net.sf.basedb.core.query.HqlInnerJoin

getChildren() - Method in class net.sf.basedb.core.query.HqlLeftJoin

getChildren() - Method in class net.sf.basedb.core.query.HqlPropertyExpression

getChildren() - Method in class net.sf.basedb.core.query.HqlRightJoin

getChildren() - Method in class net.sf.basedb.core.query.HqlSizeExpression

getChildren() - Method in class net.sf.basedb.core.query.IdListRestriction

getChildren() - Method in class net.sf.basedb.core.query.InRestriction

getChildren() - Method in class net.sf.basedb.core.query.IntegerExpression

getChildren() - Method in class net.sf.basedb.core.query.LikeRestriction

getChildren() - Method in class net.sf.basedb.core.query.LogExpression

getChildren() - Method in class net.sf.basedb.core.query.LteqRestriction

getChildren() - Method in class net.sf.basedb.core.query.LtRestriction

getChildren() - Method in class net.sf.basedb.core.query.MaxExpression

getChildren() - Method in class net.sf.basedb.core.query.MeanExpression

getChildren() - Method in class net.sf.basedb.core.query.MinExpression

getChildren() - Method in class net.sf.basedb.core.query.MultiplyExpression

getChildren() - Method in class net.sf.basedb.core.query.NegateExpression

getChildren() - Method in class net.sf.basedb.core.query.NeqRestriction

getChildren() - Method in class net.sf.basedb.core.query.NotRestriction

getChildren() - Method in class net.sf.basedb.core.query.OrRestriction

getChildren() - Method in class net.sf.basedb.core.query.ParameterExpression

getChildren() - Method in class net.sf.basedb.core.query.PermissionRestriction

getChildren() - Method in class net.sf.basedb.core.query.PowerExpression

getChildren() - Method in class net.sf.basedb.core.query.QuadraticMeanExpression

getChildren() - Method in interface net.sf.basedb.core.query.QueryElement

Get the children of this query element or null if it has no children.

getChildren() - Method in class net.sf.basedb.core.query.ReporterListExpression

getChildren() - Method in class net.sf.basedb.core.query.RlikeRestriction

getChildren() - Method in class net.sf.basedb.core.query.SelectedExpression

getChildren() - Method in class net.sf.basedb.core.query.SharedToRestriction

getChildren() - Method in class net.sf.basedb.core.query.SqlColumnExpression

getChildren() - Method in class net.sf.basedb.core.query.SqrtExpression

getChildren() - Method in class net.sf.basedb.core.query.SubqueryExpression

getChildren() - Method in class net.sf.basedb.core.query.SubtractExpression

getChildren() - Method in class net.sf.basedb.core.query.SumExpression

getChildren() - Method in class net.sf.basedb.core.query.ToDateExpression

getChildren() - Method in class net.sf.basedb.core.query.VirtualColumnExpression

getChildren() - Method in class net.sf.basedb.core.query.VirtualColumnExpression.WrappedExpression

getChildren() - Method in class net.sf.basedb.core.RawBioAssayPropertyExpression

getChildren() - Method in class net.sf.basedb.core.RawDataPropertyExpression

getChildren() - Method in class net.sf.basedb.core.RealJoin

getChildren() - Method in class net.sf.basedb.core.ReporterListJoin

getChildren() - Method in class net.sf.basedb.core.ReporterPropertyExpression

getChildren() - Method in class net.sf.basedb.util.overview.Node

Get all child nodes of this node.

getChildren() - Method in class net.sf.basedb.util.Tree.Entry

Get the list of entries for the children to this node.

getChildReporterPositions() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo

Get a map with all added child position/reporter mappings.

getChildSamples() - Method in class net.sf.basedb.core.Sample

Creates a query that returns all child (pooled) samples that has this sample as one of it's sources.

getChildWarnings() - Method in class net.sf.basedb.util.overview.Node

Get the number of warnings to children of this node.

getCircularRef(Node, BasicItem) - Static method in class net.sf.basedb.util.overview.OverviewUtil

Find the first parent node that has a reference to the given item.

getCity() - Method in class net.sf.basedb.util.GeoLocation

getClasses() - Static method in class net.sf.basedb.core.ExtendedProperties

Get a list with the name of all classes.

getClassLoader() - Method in class net.sf.basedb.core.hibernate.SessionFactoryConfiguration

Deprecated.

Get the schema.

getClassLoader() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration

Get the class loader used for accessing mapped classes.

getClassLoader() - Method in class net.sf.basedb.util.extensions.ExtensionContext

The class loader is the class loader that loaded the action factory of the extension.

getClassLoader() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext

The class loader is the class loader that loaded the action class of the extension point.

getClassLoader() - Method in class net.sf.basedb.util.extensions.InvokationContext

Get the class loader that is used for the given extension or extension point.

getClassLoader() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile

Get the class loader used to load classes for the extension.

getClassLoader() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension

getClassLoader() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint

getClassMapping(String) - Static method in class net.sf.basedb.core.HibernateUtil

getClassMappings() - Static method in class net.sf.basedb.core.HibernateUtil

getClassMetadata(String) - Static method in class net.sf.basedb.core.HibernateUtil

getClassName() - Method in class net.sf.basedb.core.data.PluginDefinitionData

Get the class name of the Java class that implements this plugin.

getClassName() - Method in class net.sf.basedb.core.PluginDefinition

Get the class name of the Java class that implements this plugin.

getClassName() - Method in class net.sf.basedb.util.extensions.xml.PluginInfo

Get the class name of the plug-in.

getClazz() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

getClazz() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction

Optional HTML class attribute that is used to style the column through CSS.

getClazz() - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo

Get a class attribute that can used to style the input field.

getClazz() - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

getClazz() - Method in interface net.sf.basedb.clients.web.extensions.menu.MenuItemAction

Class attribute to add to the main menu tag.

getClazz() - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean

getClazz() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory

getClazz() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab

getClazz() - Method in interface net.sf.basedb.clients.web.extensions.tabcontrol.TabAction

Class attribute of the main tab tag.

getClazz() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean

getClazz() - Method in interface net.sf.basedb.clients.web.extensions.toolbar.ButtonAction

Class attribute of the main button tag.

getClazz() - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean

getClazz() - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory

getClazz() - Method in class net.sf.basedb.clients.web.taglib.Body

getClazz() - Method in class net.sf.basedb.clients.web.taglib.ExceptionCatcher

getClazz() - Method in class net.sf.basedb.clients.web.taglib.StylableTag

getClazz() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab

getClazz() - Method in class net.sf.basedb.clients.web.taglib.table.Button.ButtonActionWrapper

getClazz() - Method in class net.sf.basedb.clients.web.taglib.table.Cell

getClazz() - Method in class net.sf.basedb.clients.web.taglib.table.CellValue

getClearState() - Method in class net.sf.basedb.core.PluginResponse

If set after a job configuration sequence, the saved state should be cleared before starting the job.

getClient() - Method in class net.sf.basedb.core.ClientDefaultSetting

Get the client application this setting is valid for.

getClient() - Method in class net.sf.basedb.core.data.ChangeHistoryData

getClient() - Method in class net.sf.basedb.core.data.ClientDefaultSettingData

Get the client application this setting is valid for.

getClient() - Method in class net.sf.basedb.core.data.ContextData

Get the client which uses this context.

getClient() - Method in class net.sf.basedb.core.data.ContextIndex

Get the client which uses this context.

getClient() - Method in class net.sf.basedb.core.data.HelpData

Get the client for this help text.

getClient() - Method in class net.sf.basedb.core.data.SessionData

Get the client application the user was using.

getClient() - Method in class net.sf.basedb.core.data.UserClientSettingData

Get the client application this setting is valid for.

getClient() - Method in class net.sf.basedb.core.data.UserDeviceData

Get the client application this device is associated with.

getClient() - Method in class net.sf.basedb.core.Help

Get the client application this setting is valid for.

getClient() - Method in class net.sf.basedb.core.Session

Get the client application the user was using in this session.

getClient() - Method in class net.sf.basedb.core.UserClientSetting

Get the client application this setting is valid for.

getClient() - Method in class net.sf.basedb.core.UserDevice

Get the client application the user was using with this device.

getClient(DbControl) - Method in class net.sf.basedb.core.ChangeHistory

Load the client application that was used when the change was made.

getClient(DbControl) - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo

Load the client application that was used in the transaction.

getClient(DbControl, ChangeHistory, boolean, boolean) - Static method in class net.sf.basedb.clients.web.ChangeHistoryUtil

Get the client application that was used to make the change in HTML format.

getClientAliases(String, Principal[]) - Method in class net.sf.basedb.util.ssl.StaticKeyManager

getClientCertificate() - Method in class net.sf.basedb.core.data.FileServerData

Get the client certificate that we need to send to the server to make the server accept our connection.

getClientCertificate() - Method in class net.sf.basedb.core.FileServer

Get the client certificate that BASE should use to authenticate with the server when connecting with https.

getClientCertificate() - Method in class net.sf.basedb.util.uri.ConnectionParameters

Get the client certificate that BASE should use to authenticate with the server when connecting using SSL.

getClientCertificatePassword() - Method in class net.sf.basedb.core.data.FileServerData

Get the password that is used to unlock the client certificate.

getClientCertificatePassword() - Method in class net.sf.basedb.core.FileServer

Get the password that is needed to unlock the client certificate.

getClientCertificatePassword() - Method in class net.sf.basedb.util.uri.ConnectionParameters

Get the password that is needed to unlock the client certificate.

getClientContext() - Method in class net.sf.basedb.util.extensions.ExtensionContext

getClientContext() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext

getClientContext() - Method in class net.sf.basedb.util.extensions.ExtensionsInvoker

Get the client context that is used by this invoker.

getClientContext() - Method in class net.sf.basedb.util.extensions.InvokationContext

Get the client context that was passed to the Registry.useExtensions(ClientContext, ExtensionsFilter, String...) method.

getClientDefaultSetting(String) - Method in class net.sf.basedb.core.SessionControl

Get the value of the ClientDefaultSetting with the specified name.

getClientId() - Method in class net.sf.basedb.core.ChangeHistory

Get the ID of the client application that was used to make the change.

getClientId() - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo

Get the ID of the client application that was used in the transaction.

getClientId() - Method in class net.sf.basedb.core.data.ChangeHistoryData

The ID of the client application the user used to make the change.

getClientId() - Method in class net.sf.basedb.core.log.TransactionDetails

Get the ID of the client appliction that is used, or 0 if not known.

getClientId() - Method in class net.sf.basedb.core.SessionControl

Get the id of the Client application that created this SessionControl.

getClientName() - Method in class net.sf.basedb.core.SessionControl

Get the name of the Client application that created this SessionControl.

getClientSettings() - Method in class net.sf.basedb.core.data.UserData

This is the inverse end.

getClientSettings(Client) - Method in class net.sf.basedb.core.User

Get a query that returns the settings for the specified client.

getClientWithExternalId(String) - Method in class net.sf.basedb.core.SessionControl

getClientX509Certificate() - Method in class net.sf.basedb.core.FileServer

Get the X.509 certificate for the client.

getClonableProperties() - Method in class net.sf.basedb.core.ReporterCloneTemplate

Get a list with all clonable properties in this template.

getClonableProperties(ReporterCloneTemplateData) - Static method in class net.sf.basedb.core.ReporterCloneTemplate

getClonableProperty(String) - Method in class net.sf.basedb.core.ReporterCloneTemplate

Get information about a clonable property that is included in this template.

getClone() - Method in class net.sf.basedb.util.annotations.InheritSpecification

getClonedSelectSql(VirtualDb) - Static method in class net.sf.basedb.core.Reporter

Generate an SQL statement for selecting ALL reporter properties from a cloned table.

getCmd() - Method in class net.sf.basedb.clients.jobagent.CmdLine

Get the command parameter

getCollected() - Method in class net.sf.basedb.util.listable.CollectExtracts

Get all extracts that has been collected.

getCollectedChildren() - Method in class net.sf.basedb.util.listable.CollectExtracts

Get child extracts that was collected by the CollectExtracts.collectChildrenOfCollected(boolean) and/or CollectExtracts.collectChildrenOfSource(boolean) collectors.

getCollectedParents() - Method in class net.sf.basedb.util.listable.CollectExtracts

Get parent extracts that was collected by the CollectExtracts.collectParentsOfSource(boolean) or CollectExtracts.collectParentsOfCollected(boolean) collector.

getCollectionFormatter() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

getCollectionFormatter() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction

Get a formatter that is intended to format a collection of values that have been retrieved from this action.

getCollectionSeparatorParameter() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport

getColor() - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup

Get a color code for HTML that is as distinct as possible from the color of the other groups.

getColor(float) - Method in class net.sf.basedb.util.ColorGenerator

Get the color for the value.

getColor(String) - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey

getColorFormatter(SessionControl, Coloring, Formatter<Number>) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory

Get a formatter that adds a color box to the display which is a visual representation of the value.

getColorGenerator(SessionControl, Coloring) - Static method in class net.sf.basedb.clients.web.Base

getColoring() - Method in class net.sf.basedb.core.data.ExtraValueTypeData

Get the coloring information for this extra value type.

getColoring() - Method in class net.sf.basedb.core.data.FormulaData

Get the coloring information for this formula.

getColoring() - Method in class net.sf.basedb.core.ExtraValueType

Get coloring information for this extra value.

getColoring() - Method in class net.sf.basedb.core.Formula

Get coloring information for this formula.

getColspan() - Method in class net.sf.basedb.clients.web.taglib.table.Header

getColumn() - Method in class net.sf.basedb.clients.web.taglib.table.Cell

getColumn() - Method in class net.sf.basedb.core.BioWell

Gets the column index where this well is located.

getColumn() - Method in class net.sf.basedb.core.data.BioWellData

The column coordinate of this well.

getColumn() - Method in class net.sf.basedb.core.data.FeatureData

Get the column coordinate of the feature.

getColumn() - Method in class net.sf.basedb.core.data.MappingCoordinate

Get the column number.

getColumn() - Method in class net.sf.basedb.core.data.PlateCoordinate

Get the column number.

getColumn() - Method in class net.sf.basedb.core.data.RawData

getColumn() - Method in class net.sf.basedb.core.data.ReporterClonePropertyData

Get the name of database column.

getColumn() - Method in class net.sf.basedb.core.data.WellData

The column coordinate of this well.

getColumn() - Method in class net.sf.basedb.core.ExtendedProperty

Get the database column of the extended property.

getColumn() - Method in class net.sf.basedb.core.FeatureCoordinate

getColumn() - Method in class net.sf.basedb.core.VirtualColumn

Get the database column name of the column.

getColumn() - Method in class net.sf.basedb.core.Well

Get the column coordinate of this well on the plate.

getColumn(String) - Static method in class net.sf.basedb.core.RawBioAssayPropertyExpression

getColumn(String) - Static method in class net.sf.basedb.core.ReporterPropertyExpression

getColumn(RawDataType, String) - Static method in class net.sf.basedb.core.RawDataPropertyExpression

Get the database column name for the specified property of the specified raw data type.

getColumnContent() - Method in class net.sf.basedb.clients.web.taglib.table.Table

getColumnCount() - Method in class net.sf.basedb.util.bfs.AnnotationModel

Get the number of column.

getColumnCount() - Method in class net.sf.basedb.util.bfs.AnnotationWriter

Get the number of data columns.

getColumnCount() - Method in class net.sf.basedb.util.bfs.DataWriter

Get the number of data columns.

getColumnCount() - Method in class net.sf.basedb.util.bfs.MatrixModel

Get the number of columns.

getColumnFormatter(int) - Method in class net.sf.basedb.util.export.TableWriter

getColumnHeaderIndex(String) - Method in class net.sf.basedb.util.parser.FlatFileParser

Get the index of a column header with a given name.

getColumnHeaders() - Method in class net.sf.basedb.util.parser.FlatFileParser

Get all column headers that were found by splitting the line matching the FlatFileParser.setDataHeaderRegexp(Pattern) pattern using the FlatFileParser.setDataSplitterRegexp(Pattern) pattern.

getColumnIndex(String) - Method in class net.sf.basedb.util.bfs.AnnotationModel

Get the column index for a given header.

getColumnMappingParameterName() - Method in class net.sf.basedb.plugins.batchimport.AnnotationIdMethod

getColumnMappingParameterName() - Method in class net.sf.basedb.plugins.batchimport.FallbackIdMethod

getColumnMappingParameterName() - Method in class net.sf.basedb.plugins.batchimport.FileImporter.PathIdMethod

getColumnMappingParameterName() - Method in interface net.sf.basedb.plugins.batchimport.IdMethod

getColumnMappingParameterName() - Method in class net.sf.basedb.plugins.batchimport.InternalIdMethod

getColumnMappingParameterName() - Method in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod

getColumnMappingParameterName() - Method in class net.sf.basedb.plugins.batchimport.PropertyIdMethod

getColumnName(RawDataProperty, RawBioAssay) - Static method in class net.sf.basedb.plugins.IlluminaRawDataImporter

Convert a raw data property to a column name.

getColumnNo() - Method in class net.sf.basedb.core.data.DataCubeColumnData

The column number of this column in the data cube.

getColumnNo() - Method in class net.sf.basedb.core.DataCubeColumn

Get the number of this column.

getColumnPrefixParameter() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport

getColumnRestriction(PropertyFilter) - Method in interface net.sf.basedb.core.query.QueryFilterAction

Generate a restriction for the given filter.

getColumns() - Method in class net.sf.basedb.clients.web.taglib.table.Table

getColumns() - Method in class net.sf.basedb.core.BioPlate

Get the number of rows on this plate.

getColumns() - Method in class net.sf.basedb.core.data.DataCubeData

This is the inverse end.

getColumns() - Method in class net.sf.basedb.core.data.PlateGeometryData

The number of rows in this geometry.

getColumns() - Method in class net.sf.basedb.core.dbengine.TableInfo

Get information about the columns in the table.

getColumns() - Method in class net.sf.basedb.core.dbengine.TableInfo.IndexInfo

getColumns() - Method in class net.sf.basedb.core.dbengine.TableInfo.PrimaryKeyInfo

getColumns() - Method in class net.sf.basedb.core.PlateGeometry

Get the number of columns in this geometry.

getColumns(Experiment) - Method in enum class net.sf.basedb.core.VirtualTable

Get all columns in this table.

getColumns(VirtualDb) - Method in enum class net.sf.basedb.core.VirtualTable

Get all columns in this table.

getColumnSeparator() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil

Get the current column separator.

getColumnsFile(TableInfo) - Method in class net.sf.basedb.core.Migration

Get the columns file for the given table.

getColumnSubtitles() - Method in class net.sf.basedb.clients.web.taglib.table.Table

getCommand() - Method in class net.sf.basedb.core.plugin.NamespaceRequestWrapper

getCommand() - Method in interface net.sf.basedb.core.plugin.Request

The command the plugin should execute.

getCommand() - Method in class net.sf.basedb.core.PluginRequest

Get the command this request will issue to the plugin when PluginRequest.invoke() is called.

getCommand() - Method in class net.sf.basedb.core.PluginRequest.RequestImpl

getCommand() - Method in class net.sf.basedb.core.RequestInformation

Get the command this request information object is valid for.

getCommand() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper

getComment() - Method in class net.sf.basedb.core.authentication.LoginRequest

Get the comment to use.

getComment() - Method in class net.sf.basedb.core.BioMaterialEvent

Get the comment about this event.

getComment() - Method in class net.sf.basedb.core.data.BioMaterialEventData

Get the comment about this event.

getComment() - Method in class net.sf.basedb.core.data.PlateEventData

Get the comment about this event.

getComment() - Method in class net.sf.basedb.core.hibernate.QueryWrapper

getComment() - Method in class net.sf.basedb.core.PlateEvent

Get the comment about this event.

getCommonCharsets() - Static method in class net.sf.basedb.core.Config

Get a set containing the most common character sets used by text files.

getCommonName() - Method in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter

getCommonPrefix(Collection<String>) - Static method in class net.sf.basedb.core.StringUtil

Find the longest common prefix for a collection of strings.

getCompleted() - Method in class net.sf.basedb.core.SimpleAbsoluteProgressReporter

Get completed number of ticks of the task.

getCompressedSize() - Method in class net.sf.basedb.core.data.FileData

Get the size in bytes that this FileData object uses after compression.

getCompressedSize() - Method in class net.sf.basedb.core.File

Get the compressed size of this file.

getCondition() - Method in class net.sf.basedb.core.dbengine.TableInfo.IndexInfo

If a condition is specificed a partial index is created for rows that matches the conditions.

getCondition() - Method in class net.sf.basedb.core.query.WhenStatement

Get the condition of this statement.

getConfigDirectory() - Static method in class net.sf.basedb.core.Config

Get the directory where the BASE configuration files are located.

getConfigurationInstallOption(int) - Method in class net.sf.basedb.plugins.PluginConfigurationImporter

Returns if a configuration in a certain place/order in the XML-file should be imported

getConfigurations() - Method in class net.sf.basedb.core.data.PluginDefinitionData

This is the inverse end.

getConfigurationValues() - Method in class net.sf.basedb.core.data.PluginConfigurationData

Used by Hibernate to link with configuration values.

getConfigurationValues() - Method in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget

getConfiguredColors(SessionControl) - Static method in class net.sf.basedb.clients.web.Base

getConfiguredJobParameters() - Method in class net.sf.basedb.plugins.HelpImporter

getConfiguredJobParameters() - Method in class net.sf.basedb.plugins.PluginConfigurationImporter

getConfiguredQuery(DbControl, ItemContext, boolean, ItemQuery<T>, ModeInfo) - Static method in class net.sf.basedb.clients.web.Base

Deprecated.

In 3.18, use Base.getConfiguredQuery(DbControl, ItemContext, ClientContext, boolean, ItemQuery, ModeInfo) instead

getConfiguredQuery(DbControl, ItemContext, ClientContext, boolean, ItemQuery<T>, ModeInfo) - Static method in class net.sf.basedb.clients.web.Base

Configures a query.

getConfiguredSelectionParameters() - Method in class net.sf.basedb.plugins.PluginConfigurationImporter

Gets request information to set which configuration to import

getConfigureExecutorParameters(String) - Method in class net.sf.basedb.plugins.executor.BaseFileExporterSupport

getConfigureExecutorParameters(String) - Method in class net.sf.basedb.plugins.executor.BaseFileImporterSupport

getConfigureExecutorParameters(String) - Method in class net.sf.basedb.plugins.executor.BfsExporterSupport

getConfigureExecutorParameters(String) - Method in class net.sf.basedb.plugins.executor.BfsImporterSupport

getConfigureExecutorParameters(String) - Method in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport

getConfigureExportImportPluginParameters() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

getConfigureExternalParameters() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

getConfigureImportParameters(GuiContext) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter

Step 3 of 3.

getConfigureJobParameters() - Method in class net.sf.basedb.plugins.Base1PluginExecuter

Creates the information needed for job configuration and initiates the parameters.

getConfigureJobParameters() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

getConfigureJobParameters() - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin

getConfigureJobParameters() - Method in class net.sf.basedb.plugins.JepExtraValueCalculator

getConfigureJobParameters() - Method in class net.sf.basedb.plugins.LowessNormalization

getConfigureJobParameters() - Method in class net.sf.basedb.plugins.MedianRatioNormalization

getConfigureJobParameters(Boolean) - Method in class net.sf.basedb.plugins.GalExporter

getConfigureJobParameters(Boolean) - Method in class net.sf.basedb.plugins.HelpExporter

getConfigureJobParameters(Boolean) - Method in class net.sf.basedb.plugins.PluginConfigurationExporter

getConfigureJobParameters(String) - Method in class net.sf.basedb.plugins.executor.BaseFileImporterSupport

getConfigureJobParameters(String) - Method in class net.sf.basedb.plugins.executor.BfsImporterSupport

getConfigureJobParameters(String) - Method in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport

getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.clients.web.plugins.SimpleExport

getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.BfsExporterPlugin

getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.CdfFileReporterImporter

getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.FormulaFilter

getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter

getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.JepIntensityTransformer

getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator

getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.ManualTransformCreator

getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.PlateFlatFileImporter

getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.PlateMappingImporter

getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter

getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter

getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter

getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker

getConfigureJobParameters(GuiContext, Boolean) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin

getConfigureJobParameters(GuiContext, Boolean) - Method in class net.sf.basedb.plugins.PackedFileExporter

getConfigureJobParameters(GuiContext, Boolean) - Method in class net.sf.basedb.plugins.PlateMappingExporter

getConfigureMappingParameters(GuiContext) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter

Step 2 of 3.

getConfigureOptionsParameters(GuiContext) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

getConfigureOptionsParameters(GuiContext) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

getConfigureParserParameters(GuiContext, boolean) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter

getConfigureParserParameters(GuiContext, boolean) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

getConfigureParserParameters(GuiContext, boolean) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

getConfigureParserParameters(RawDataType) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter

getConfigurePluginParameters() - Method in class net.sf.basedb.plugins.Base1PluginExecuter

Creates the information needed for plugin configuration and initiates the parameters.

getConfigurePluginParameters() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

getConfigurePluginParameters() - Method in class net.sf.basedb.plugins.PackedFileExporter

getConfigurePluginParameters(GuiContext) - Method in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter

getConfigurePluginParameters(GuiContext) - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator

getConfigurePluginParameters(GuiContext) - Method in class net.sf.basedb.plugins.ManualTransformCreator

getConfigurePluginParameters(GuiContext) - Method in class net.sf.basedb.plugins.PlateFlatFileImporter

getConfigurePluginParameters(GuiContext) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter

getConfigurePluginParameters(GuiContext) - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

getConfigureRawDataTypeParameters() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter

getConnection(Integer) - Method in class net.sf.basedb.core.JobAgent

Get a connection object for connecting to the job agent.

getConnection(Session) - Static method in class net.sf.basedb.core.HibernateUtil

Get the underlying JDBC connection from the Hibernate session.

getConnectionManagerFactory() - Method in class net.sf.basedb.core.data.FileServerData

Get the ID of the connection manager factory that should be used to retreieve the file contents and metadata.

getConnectionManagerFactoryId() - Method in class net.sf.basedb.core.FileServer

Get the ID of the connection manager factory that should be used to access file contents and metadata.

getConnectionManagerFactoryId() - Method in class net.sf.basedb.util.uri.ConnectionParameters

Get the connection manager factory that we should use to access the file, or null to use auto-detection.

getConnectionProperties() - Static method in class net.sf.basedb.core.HibernateUtil

Read database configuration properties from the base.config file and map them to Hibernate settings.

getConstructor() - Method in enum class net.sf.basedb.core.Item

Get the default constructor for new objects of this type.

getContact() - Method in class net.sf.basedb.core.data.PluginDefinitionData

Get contact information for the plugin.

getContact() - Method in interface net.sf.basedb.core.plugin.About

Contact information to get more information about the plugin.

getContact() - Method in class net.sf.basedb.core.plugin.AboutImpl

getContact() - Method in class net.sf.basedb.core.PluginDefinition

Get contact information for the plugin.

getContact() - Method in class net.sf.basedb.util.extensions.AboutBean

getContact() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout

getContent() - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory.Section

getContent() - Method in interface net.sf.basedb.clients.web.extensions.section.SectionAction

Get the (HTML) contents of the section.

getContent() - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean

getContent() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory

getContent() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab

getContent() - Method in interface net.sf.basedb.clients.web.extensions.tabcontrol.TabAction

Get the (HTML) contents of the tab.

getContent() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean

getContent() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab

getContentLength(HttpResponse) - Static method in class net.sf.basedb.util.HttpUtil

Get the content length from the headers in the response.

getContentstyle() - Method in class net.sf.basedb.clients.web.taglib.HideableSection

getContentstyle() - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl

getContentStyle() - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory.Section

getContentStyle() - Method in interface net.sf.basedb.clients.web.extensions.section.SectionAction

Extra CSS style attributes that will be added to the style attribute of the content section tag.

getContentStyle() - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean

getContentType(HttpResponse) - Static method in class net.sf.basedb.util.HttpUtil

Get the content type of the content from the headers in the response.

getContext() - Method in class net.sf.basedb.clients.web.taglib.HideableSection

getContext(int) - Method in class net.sf.basedb.core.SessionControl

Load a context without making it the current context.

getContextId() - Method in class net.sf.basedb.core.ItemContext

Get the database ID of this context.

getContextItem() - Method in class net.sf.basedb.core.data.JobData

The item type of the context that was active when configuring this job. null = no context was known

getContextMessage() - Method in class net.sf.basedb.util.ContextUtil.ContextResult

Get the warning level message, or the message from Throwable.getMessage() if this is an error-level object.

getContextMessages(Collection<ContextUtil.ContextResult>, boolean, boolean) - Static method in class net.sf.basedb.util.ContextUtil

Get all messages from plug-in / configurations combinations that can't be used.

getContextNames(Item) - Method in class net.sf.basedb.core.SessionControl

Same as: getContextNames(item, getCurrentSubcontext(item))

getContextNames(Item, String) - Method in class net.sf.basedb.core.SessionControl

Get a list with the names of all named contexts for a given item and subcontext.

getContexts() - Method in class net.sf.basedb.core.data.ClientData

This is the inverse end.

getContexts() - Method in class net.sf.basedb.core.data.UserData

The saved contexts for the user.

getContextType() - Method in class net.sf.basedb.core.data.GuiContextData

getContextType() - Method in class net.sf.basedb.core.data.JobData

The context type that was active when configuring this job. 0 = single item, 1 = list

getConvertedValue(String, Method) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader

getConverter(Object) - Static method in class net.sf.basedb.util.jep.convert.ConverterFactory

Get a converter for the specified built-in JEP object.

getConverter(PostfixMathCommandI, Operator) - Method in class net.sf.basedb.util.jep.convert.ASTFunNodeConverter

Get a converter by first checking the if one exists for the given function, and then for the given operator symbol.

getConverterByClass(Object) - Static method in class net.sf.basedb.util.jep.convert.ConverterFactory

Get a converter for the specified built-in JEP object by checking if a converter has been registered for it's class.

getConverters() - Static method in class net.sf.basedb.util.jep.convert.ConverterFactory

Get all registered converters.

getCookie(HttpServletRequest, String) - Static method in class net.sf.basedb.clients.web.Base

Get the cookie with the specified name.

getCookieValue(HttpServletRequest, String) - Static method in class net.sf.basedb.clients.web.Base

Get the value of the cookie with the specified name.

getCoordinate() - Method in class net.sf.basedb.core.BioWell

Get a string representation of the coordinate for this well.

getCoordinateType() - Method in class net.sf.basedb.core.data.DataCubeExtraValueData

If the extra value is a spot extra value, a position extra value or a column extra value.

getCoordinateType() - Method in class net.sf.basedb.core.DataCubeExtraValue

Get the coordinate type the extra values are attached to.

getCoordinateType() - Method in class net.sf.basedb.core.ExtraValue

Get information about which coordinates in the data cube the extra values are attached to.

getCopyAnnotationsParmeter(String, String, Boolean) - Method in class net.sf.basedb.core.plugin.AbstractPlugin

Parameter definition that asks if annotations should be copied from the plug-in definition/configuration to other items.

getCopyright() - Method in class net.sf.basedb.core.data.PluginDefinitionData

Get a copyright notice for the plugin.

getCopyright() - Method in interface net.sf.basedb.core.plugin.About

A copyright notice.

getCopyright() - Method in class net.sf.basedb.core.plugin.AboutImpl

getCopyright() - Method in class net.sf.basedb.core.PluginDefinition

Get a copyright notice for the plugin.

getCopyright() - Method in class net.sf.basedb.util.extensions.AboutBean

getCopyright() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout

getCoreTimer() - Static method in class net.sf.basedb.core.Application

getCount() - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics

Get the number of links that was found among the sampled items.

getCount() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin

Get the number of values in this bin.

getCount(int) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup

Get the number of intensity values added to the specified channel.

getCountHqlQuery(DbControl) - Method in class net.sf.basedb.core.AbstractHqlQuery

Build the count query and set parameter values for it.

getCountQuery(boolean) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter

Get a configured query that counts the number of data lines that is about to be written in a data section.

getCountQuery(DbControl, boolean) - Method in class net.sf.basedb.core.AbstractQuery

Build the query string for returning the total count.

getCountry() - Method in class net.sf.basedb.util.GeoLocation

getCpuUsage() - Method in class net.sf.basedb.core.JobAgent

Get the current CPU usage in percent of the server where the job agent is running.

getCpuUsage() - Method in class net.sf.basedb.util.jobagent.JobAgentInfo

Get the CPU usage in percent.

getCreated() - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlot

getCreated() - Method in class net.sf.basedb.core.data.JobData

Get the date and time the job was created.

getCreated() - Method in class net.sf.basedb.core.Job

Get the date and time the job was registered in the database.

getCreateForeignKeySql(String, String, String, String, Set<String>, String, Set<String>) - Method in interface net.sf.basedb.core.dbengine.DbEngine

Generates SQL that creates a foreign key constraint between two tables.

getCreateForeignKeySql(String, String, String, String, Set<String>, String, Set<String>) - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine

getCreateForeignKeySql(String, String, String, String, Set<String>, String, Set<String>) - Method in class net.sf.basedb.core.dbengine.MySQLEngine

Generate alter table schema.table add constraint name foreign key (columns) references refTable (refColumns)

getCreateForeignKeySql(String, String, String, String, Set<String>, String, Set<String>) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine

Generate alter table schema.table add constraint name foreign key (columns) references refTable (refColumns)

getCreateIndexSql(String, String, String, String, Set<String>, boolean) - Method in interface net.sf.basedb.core.dbengine.DbEngine

Generate SQL to create an index.

getCreateIndexSql(String, String, String, String, Set<String>, boolean) - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine

Generates create [unique] index <name> on <catalog>.<schema>.<table> (<columns>) which should work for most databases.

getCreateIndexSql(String, String, String, String, Set<String>, boolean) - Method in class net.sf.basedb.core.dbengine.MySQLEngine

Generate alter table <catalog>.<table> add [unique] index <name> (<columns>).

getCreateIndexSql(String, String, String, String, Set<String>, boolean) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine

Generate alter table <schema>.<table> add constraint <name> unique (<columns>) for a unique index, create index <name> on <schema>.<table> (<columns>) for other indexes.

getCreatePartialIndexSql(String, String, String, String, Set<String>, String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine

Default implementation returns a regular non-unique index.

getCreatePartialIndexSql(String, String, String, String, Set<String>, String) - Method in interface net.sf.basedb.core.dbengine.DbEngine

Generate SQL to create a partial index.

getCreatePartialIndexSql(String, String, String, String, Set<String>, String) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine

Creates a partial index which is the same as a regular index + 'WHERE [condition]';

getCreatePrimaryKeySql(String, String, String, String, Set<String>) - Method in interface net.sf.basedb.core.dbengine.DbEngine

Generate SQL to create a primary key for a table.

getCreatePrimaryKeySql(String, String, String, String, Set<String>) - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine

getCreatePrimaryKeySql(String, String, String, String, Set<String>) - Method in class net.sf.basedb.core.dbengine.MySQLEngine

Generate alter table catalog.table add primary key (columns)

getCreatePrimaryKeySql(String, String, String, String, Set<String>) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine

Generate alter table schema.table add constraint name primary key (columns).

getCreateSchemaSql(String, String) - Method in interface net.sf.basedb.core.dbengine.DbEngine

Generate an SQL statement to create the given schema.

getCreateSchemaSql(String, String) - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine

Generate create schema <catalog>.<schema>.

getCreateSchemaSql(String, String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine

Generate create schema <catalog>.

getCreateSchemaSql(String, String) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine

Generate create schema <schema>.

getCreateTemporaryIdTable(String) - Method in interface net.sf.basedb.core.dbengine.DbEngine

Generate SQL for creating a temporary table with a single 'id' column that is the primary key.

getCreateTemporaryIdTable(String) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine

CREATE TEMPORARY TABLE <table> (id integer PRIMARY KEY) ON COMMIT DROP

getCreationEvent() - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData

Get the event that created this biomaterial.

getCreationEvent() - Method in class net.sf.basedb.core.data.PhysicalBioAssayData

Get the event that created this bioassay.

getCreationEvent() - Method in class net.sf.basedb.core.MeasuredBioMaterial

Get the event that represents the creation of this biomaterial.

getCreationEvent() - Method in class net.sf.basedb.core.PhysicalBioAssay

Get the event that represents the creation of this hybridization.

getCriteriaBuilder() - Method in class net.sf.basedb.core.hibernate.SessionWrapper

getCryptedPassword() - Method in class net.sf.basedb.core.data.PasswordData

Get the crypted password.

getCubeNo() - Method in class net.sf.basedb.core.data.DataCubeData

The cube number of this cube in the virtual database.

getCubeNo() - Method in class net.sf.basedb.core.DataCube

Get the number of this data cube.

getCubes() - Method in class net.sf.basedb.core.data.VirtualDbData

The number of data cubes in the virtual database.

getCubes() - Method in class net.sf.basedb.core.VirtualDb

Get the number of DataCube:s in this virtual database.

getCurrent() - Method in class net.sf.basedb.clients.web.taglib.Select

getCurrent() - Method in class net.sf.basedb.clients.web.taglib.SubtypeSelector

getCurrentBioAssaySet(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

Get the current source bioassay set.

getCurrentBioAssaySet(DbControl) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

Get the bioassay set that is used as the source for the job.

GetCurrentCatalogWork - Class in net.sf.basedb.core.hibernate

A work implementation that return the name of the current database catalog.

GetCurrentCatalogWork() - Constructor for class net.sf.basedb.core.hibernate.GetCurrentCatalogWork

Create a new work item.

getCurrentClientId() - Method in class net.sf.basedb.core.SessionControl

Get the id of the Client application that checked out this SessionControl from Application.getSessionControl(String, String, String, boolean).

getCurrentClientName() - Method in class net.sf.basedb.core.SessionControl

Get the name of the Client application that checked out this SessionControl from Application.getSessionControl(String, String, String, boolean).

getCurrentConfiguration(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractPlugin

Get the plug-in configuration that this is currently in use or null.

getCurrentConfigurationParameterValues(String) - Method in class net.sf.basedb.core.PluginRequest

Get the values that are currently stored in the plugin configuration related to this request.

getCurrentContext() - Method in class net.sf.basedb.clients.web.extensions.JspContext

Get the current item context.

getCurrentContext(Item) - Method in class net.sf.basedb.core.SessionControl

Same as: getCurrentContext(item, null, null).

getCurrentContext(Item, String) - Method in class net.sf.basedb.core.SessionControl

Same as: getCurrentContext(item, subContext, null).

getCurrentContext(Item, String, ItemContext) - Method in class net.sf.basedb.core.SessionControl

Get the current context.

getCurrentContext(Item, ItemContext) - Method in class net.sf.basedb.core.SessionControl

Same as: getCurrentContext(item, null, defaultContext).

getCurrentDerivedBioAssay(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

Get the current source derived bioassay.

getCurrentDirectory(DbControl) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker

Get the current directory or null there is no current or it can't be loaded.

getCurrentExcelWorkbook() - Method in class net.sf.basedb.util.parser.FlatFileParser

If the input stream that is being parsed is an Excel document, this method returns information about it.

getCurrentExperiment(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

Get the current experiment from information in the current context: SessionControl.getCurrentContext(Item.EXPERIMENT).

getCurrentExtension() - Method in class net.sf.basedb.util.extensions.ClientContext

Get the currently active extension point.

getCurrentExtensionPoint() - Method in class net.sf.basedb.util.extensions.ClientContext

Get the currently active extension point.

getCurrentExternalClientId() - Method in class net.sf.basedb.core.SessionControl

Get the external id of the Client application that checked out this SessionControl from Application.getSessionControl(String, String, String, boolean).

getCurrentFile() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter.FileIterator

getCurrentFile(DbControl) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker

Get the current file or null there is no current or it can't be loaded.

getCurrentFilename() - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress

Get the name of the file that is currently beeing transferred.

getCurrentItem() - Method in class net.sf.basedb.util.extensions.ClientContext

Get the currently active item.

getCurrentJob(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractPlugin

Get the job that is executing this plugin or null.

getCurrentJobParameterValues(String) - Method in class net.sf.basedb.core.PluginRequest

Get the values that are currently stored in the job related to this request.

getCurrentLine() - Method in class net.sf.basedb.util.bfs.AnnotationParser

getCurrentLine() - Method in interface net.sf.basedb.util.bfs.BfsParser

Get the current line number.

getCurrentLine() - Method in class net.sf.basedb.util.bfs.DataParser

getCurrentLine() - Method in class net.sf.basedb.util.bfs.MetadataParser

getCurrentLine() - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser

getCurrentLockMode(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

getCurrentMapper() - Static method in class net.sf.basedb.clients.web.extensions.skin.ImageRemapperUtil

Get the current image remapper.

getCurrentMatchingSource(DbControl) - Method in class net.sf.basedb.core.SyncFilter

Get the number of items that is currently matching this filter.

getCurrentNodeName() - Method in class net.sf.basedb.util.overview.node.BioWellNameGenerator

getCurrentOverview(SessionControl) - Static method in class net.sf.basedb.util.overview.OverviewUtil

Get the currently cached overview.

getCurrentParameterValue(String) - Method in class net.sf.basedb.core.PluginRequest

getCurrentParameterValues(String) - Method in class net.sf.basedb.core.PluginRequest

Get the values that are currently stored in the job or plugin configuration related to this request.

getCurrentPosition() - Method in class net.sf.basedb.util.importer.spotdata.PositionEventHandler

Get the current position.

getCurrentRawBioAssay() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter.FileIterator

getCurrentRow() - Method in class net.sf.basedb.util.excel.XlsxTableWriter

Get row that was the last one to be printed.

getCurrentSection() - Method in class net.sf.basedb.util.basefile.BaseFileWriter

getCurrentSection() - Method in class net.sf.basedb.util.bfs.MetadataWriter

Get the name of the current section.

getCurrentSessionId() - Method in class net.sf.basedb.core.SessionControl

Get the id of the current user session, or 0 if no user is logged in.

getCurrentSheet() - Method in class net.sf.basedb.util.parser.FlatFileParser

If the input stream that is being parsed is an Excel document, this method returns information about the current worksheet.

getCurrentSubcontext(SessionControl.MainContext) - Method in class net.sf.basedb.core.SessionControl

Get the currently active subcontext for the item.

getCurrentTitlePrefix() - Method in class net.sf.basedb.util.overview.node.BioWellNameGenerator

getCurrentValue(Cell) - Method in class net.sf.basedb.clients.web.taglib.table.ExtensionCells

Get the value for the current column and item and update other settings for the cell.

getCustomRequestHandlerClasses() - Method in class net.sf.basedb.clients.jobagent.Agent

getData() - Method in class net.sf.basedb.core.AnnotatedItem

getData() - Method in class net.sf.basedb.core.Annotation

getData() - Method in class net.sf.basedb.core.AnnotationSet

getData() - Method in class net.sf.basedb.core.AnnotationType

getData() - Method in class net.sf.basedb.core.AnnotationTypeCategory

getData() - Method in class net.sf.basedb.core.AnyToAny

getData() - Method in class net.sf.basedb.core.ArrayBatch

getData() - Method in class net.sf.basedb.core.ArrayDesign

getData() - Method in class net.sf.basedb.core.ArrayDesignBlock

getData() - Method in class net.sf.basedb.core.ArrayDesignPlate

getData() - Method in class net.sf.basedb.core.ArraySlide

getData() - Method in class net.sf.basedb.core.BasicItem

Get the BasicData object that holds all data for this item.

getData() - Method in class net.sf.basedb.core.BioAssay

getData() - Method in class net.sf.basedb.core.BioAssaySet

getData() - Method in class net.sf.basedb.core.BioMaterial

getData() - Method in class net.sf.basedb.core.BioMaterialEvent

getData() - Method in class net.sf.basedb.core.BioPlate

getData() - Method in class net.sf.basedb.core.BioPlateEvent

getData() - Method in class net.sf.basedb.core.BioPlateEventParticipant

getData() - Method in class net.sf.basedb.core.BioPlateEventType

getData() - Method in class net.sf.basedb.core.BioPlateType

getData() - Method in class net.sf.basedb.core.BioSource

getData() - Method in class net.sf.basedb.core.BioWell

getData() - Method in class net.sf.basedb.core.ChangeHistory

getData() - Method in class net.sf.basedb.core.Client

getData() - Method in class net.sf.basedb.core.ClientDefaultSetting

getData() - Method in class net.sf.basedb.core.CommonItem

getData() - Method in class net.sf.basedb.core.DataCube

getData() - Method in class net.sf.basedb.core.DataCubeColumn

getData() - Method in class net.sf.basedb.core.DataCubeExtraValue

getData() - Method in class net.sf.basedb.core.DataCubeFilter

getData() - Method in class net.sf.basedb.core.DataCubeLayer

getData() - Method in class net.sf.basedb.core.DataFileType

getData() - Method in class net.sf.basedb.core.DerivedBioAssay

getData() - Method in class net.sf.basedb.core.Directory

getData() - Method in class net.sf.basedb.core.DiskUsage

getData() - Method in class net.sf.basedb.core.Experiment

getData() - Method in class net.sf.basedb.core.Extract

getData() - Method in class net.sf.basedb.core.ExtraValue

getData() - Method in class net.sf.basedb.core.ExtraValueType

getData() - Method in class net.sf.basedb.core.File

getData() - Method in class net.sf.basedb.core.FileServer

getData() - Method in class net.sf.basedb.core.FileSet

getData() - Method in class net.sf.basedb.core.FileSetMember

getData() - Method in class net.sf.basedb.core.Formula

getData() - Method in class net.sf.basedb.core.GlobalDefaultSetting

getData() - Method in class net.sf.basedb.core.Group

getData() - Method in class net.sf.basedb.core.Hardware

getData() - Method in class net.sf.basedb.core.Help

getData() - Method in class net.sf.basedb.core.ItemKey

getData() - Method in class net.sf.basedb.core.ItemList

getData() - Method in class net.sf.basedb.core.ItemSubtype

getData() - Method in class net.sf.basedb.core.ItemSubtypeFileType

getData() - Method in class net.sf.basedb.core.Job

getData() - Method in class net.sf.basedb.core.JobAgent

getData() - Method in class net.sf.basedb.core.JobAgentSettings

getData() - Method in class net.sf.basedb.core.Kit

getData() - Method in class net.sf.basedb.core.MeasuredBioMaterial

getData() - Method in class net.sf.basedb.core.Message

getData() - Method in class net.sf.basedb.core.MimeType

getData() - Method in class net.sf.basedb.core.News

getData() - Method in class net.sf.basedb.core.OwnedItem

getData() - Method in class net.sf.basedb.core.PermissionTemplate

getData() - Method in class net.sf.basedb.core.PhysicalBioAssay

getData() - Method in class net.sf.basedb.core.Plate

getData() - Method in class net.sf.basedb.core.PlateEvent

getData() - Method in class net.sf.basedb.core.PlateEventType

getData() - Method in class net.sf.basedb.core.PlateGeometry

getData() - Method in class net.sf.basedb.core.PlateMapping

getData() - Method in class net.sf.basedb.core.PlateType

getData() - Method in class net.sf.basedb.core.Platform

getData() - Method in class net.sf.basedb.core.PlatformFileType

getData() - Method in class net.sf.basedb.core.PlatformVariant

getData() - Method in class net.sf.basedb.core.PluginConfiguration

getData() - Method in class net.sf.basedb.core.PluginDefinition

getData() - Method in class net.sf.basedb.core.PluginType

getData() - Method in class net.sf.basedb.core.Project

getData() - Method in class net.sf.basedb.core.ProjectKey

getData() - Method in class net.sf.basedb.core.PropertyFilter

Create a new database filter object from this filter.

getData() - Method in class net.sf.basedb.core.Protocol

getData() - Method in class net.sf.basedb.core.Quantity

getData() - Method in class net.sf.basedb.core.Quota

getData() - Method in class net.sf.basedb.core.QuotaType

getData() - Method in class net.sf.basedb.core.RawBioAssay

getData() - Method in class net.sf.basedb.core.ReporterCloneTemplate

getData() - Method in class net.sf.basedb.core.ReporterList

getData() - Method in class net.sf.basedb.core.ReporterScore

getData() - Method in class net.sf.basedb.core.ReporterType

getData() - Method in class net.sf.basedb.core.Role

getData() - Method in class net.sf.basedb.core.RoleKey

getData() - Method in class net.sf.basedb.core.RootRawBioAssay

getData() - Method in class net.sf.basedb.core.Sample

getData() - Method in class net.sf.basedb.core.Session

getData() - Method in class net.sf.basedb.core.Setting

getData() - Method in class net.sf.basedb.core.SharedItem

getData() - Method in class net.sf.basedb.core.Software

getData() - Method in class net.sf.basedb.core.SyncFilter

getData() - Method in class net.sf.basedb.core.Tag

getData() - Method in class net.sf.basedb.core.Transformation

getData() - Method in class net.sf.basedb.core.Unit

getData() - Method in class net.sf.basedb.core.User

getData() - Method in class net.sf.basedb.core.UserClientSetting

getData() - Method in class net.sf.basedb.core.UserDefaultSetting

getData() - Method in class net.sf.basedb.core.UserDevice

getData() - Method in class net.sf.basedb.core.VirtualDb

getData() - Method in class net.sf.basedb.core.Well

getData() - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser.SynchronizedData

Get the current data line, split into columns.

getData(int, int) - Method in class net.sf.basedb.util.bfs.AnnotationModel

Get the data element at a given row and column index.

getData(int, int) - Method in class net.sf.basedb.util.bfs.MatrixModel

Get the data element at a given row and column index.

getData(int, String) - Method in class net.sf.basedb.util.bfs.AnnotationModel

Get the data element at a given row and column.

getData(String, UserData, ClientData, boolean) - Method in class net.sf.basedb.core.ItemContext

Create a new database context object from this context.

getData(DbControl, ExportedProperty, I) - Method in class net.sf.basedb.clients.web.extensions.list.ListColumnDataLoader

getData(DbControl, ExportedProperty, AnnotationType) - Method in class net.sf.basedb.clients.web.plugins.AnnotationTypeEnumerationLoader

getData(DbControl, ExportedProperty, AnnotationType) - Method in class net.sf.basedb.clients.web.plugins.AnnotationTypeItemTypesLoader

getData(DbControl, ExportedProperty, BasicItem) - Method in class net.sf.basedb.clients.web.plugins.AnyToAnyDataLoader

getData(DbControl, ExportedProperty, BasicItem) - Method in class net.sf.basedb.clients.web.plugins.ItemQueryWrapper

Uses a Metadata object to get the value of the specified property.

getData(DbControl, ExportedProperty, BasicItem) - Method in class net.sf.basedb.clients.web.plugins.MapValueLoader

getData(DbControl, ExportedProperty, BioAssay) - Method in class net.sf.basedb.clients.web.plugins.BioAssayExperimentalFactorLoader

getData(DbControl, ExportedProperty, ChangeHistory) - Method in class net.sf.basedb.clients.web.plugins.ChangeHistoryDetailLoader

getData(DbControl, ExportedProperty, ChangeHistory) - Method in class net.sf.basedb.clients.web.plugins.ChangeHistoryItemLoader

getData(DbControl, ExportedProperty, BasicData) - Method in class net.sf.basedb.clients.web.plugins.DataQueryWrapper

Uses a Metadata object to get the value of the specified property.

getData(DbControl, ExportedProperty, FileStoreEnabled) - Method in class net.sf.basedb.clients.web.plugins.FileSetMemberLoader

getData(DbControl, ExportedProperty, MeasuredBioMaterial) - Method in class net.sf.basedb.clients.web.plugins.ParentBioMaterialEventSourceLoader

getData(DbControl, ExportedProperty, MeasuredBioMaterial) - Method in class net.sf.basedb.clients.web.plugins.ParentBioMaterialLoader

getData(DbControl, ExportedProperty, Nameable) - Method in class net.sf.basedb.clients.web.plugins.PathLoader

getData(DbControl, ExportedProperty, PhysicalBioAssay) - Method in class net.sf.basedb.clients.web.plugins.ParentBioMaterialEventSourceLoaderFromBioAssay

getData(DbControl, ExportedProperty, SqlResult) - Method in class net.sf.basedb.clients.web.plugins.DynamicQueryWrapper

Calls SqlResult.getObject(int) and increases the column index for each call.

getData(DbControl, ExportedProperty, ReporterScore) - Method in class net.sf.basedb.clients.web.plugins.ReporterScoreQueryWrapper

Uses a Metadata object to get the value of the specified property.

getData(DbControl, ExportedProperty, T) - Method in interface net.sf.basedb.clients.web.plugins.DataLoader

Get the value for the specified property.

getData(DbControl, ExportedProperty, T) - Method in class net.sf.basedb.clients.web.plugins.ItemQueryLoader

getDatabaseVersionString() - Static method in class net.sf.basedb.core.Application

Gets the version of the database server

getDataByName(Session, int, Item, String) - Static method in class net.sf.basedb.core.AnyToAny

Get an any-to-any link.

getDataClass() - Method in enum class net.sf.basedb.core.Item

Get the data object that is used to store information in the database for items of this type.

getDataClassName(Object) - Static method in class net.sf.basedb.core.log.EntityDetails

getDataCube() - Method in class net.sf.basedb.core.BioAssaySet

Get the data cube this biossayset stores it's data in.

getDataCube() - Method in class net.sf.basedb.core.data.DataCubeColumnData

Get the data cube this column belongs to.

getDataCube() - Method in class net.sf.basedb.core.data.DataCubeExtraValueData

Get the data cube this filter belongs to.

getDataCube() - Method in class net.sf.basedb.core.data.DataCubeFilterData

Get the data cube this filter belongs to.

getDataCube() - Method in class net.sf.basedb.core.data.DataCubeLayerData

Get the data cube this layer belongs to.

getDataCube() - Method in class net.sf.basedb.core.DataCubeColumn

Get the data cube this layer belongs to.

getDataCube() - Method in class net.sf.basedb.core.DataCubeExtraValue

Get the data cube this extra value belongs to.

getDataCube() - Method in class net.sf.basedb.core.DataCubeFilter

Get the data cube this filter belongs to.

getDataCube() - Method in class net.sf.basedb.core.DataCubeLayer

Get the data cube this layer belongs to.

getDataCube() - Method in class net.sf.basedb.core.DynamicQuery

getDataCube() - Method in class net.sf.basedb.core.ExtraValue

getDataCubeColumn() - Method in class net.sf.basedb.core.BioAssay

Get the DataCubeColumn object where this bioassay store it's data.

getDataCubeColumn() - Method in class net.sf.basedb.core.data.BioAssayData

Get the column this bioassay stores it's data in.

getDataCubeColumnNo() - Method in class net.sf.basedb.core.BioAssay

Get the column coordinate in the data cube that this bioassay stores it's data in.

getDataCubeExtraValue() - Method in class net.sf.basedb.core.data.ExtraValueData

Get the data cube extra value where the extra values are stored.

getDataCubeExtraValue() - Method in class net.sf.basedb.core.ExtraValue

getDataCubeFilter() - Method in class net.sf.basedb.core.BioAssaySet

Get the data cube filter this biossayset uses to filter spot data.

getDataCubeFilter() - Method in class net.sf.basedb.core.data.BioAssaySetData

Get the filter used by this bioassayset.

getDataCubeFilterNo() - Method in class net.sf.basedb.core.BioAssaySet

Get the number of the filter that this bioassayset is using, or 0 if no filter is used.

getDataCubeLayer() - Method in class net.sf.basedb.core.BioAssaySet

Get the data cube layer this biossayset stores it's data in.

getDataCubeLayer() - Method in class net.sf.basedb.core.data.BioAssaySetData

Get the layer this bioassayset stores it's data in.

getDataCubeLayerNo() - Method in class net.sf.basedb.core.BioAssay

Get the layer coordinate in the data cube that this bioassay stores it's data in.

getDataCubeLayerNo() - Method in class net.sf.basedb.core.BioAssaySet

Get the layer coordinate in the data cube that this bioassayset stores it's data in.

getDataCubeNo() - Method in class net.sf.basedb.core.BioAssay

Get the number of the data cube this bioassay stores it's data in.

getDataCubeNo() - Method in class net.sf.basedb.core.BioAssaySet

Get the number of the data cube this bioassayset stores it's data in.

getDataCubeNo() - Method in class net.sf.basedb.core.DataCubeColumn

Get the number of the data cube this layer belongs to.

getDataCubeNo() - Method in class net.sf.basedb.core.DataCubeExtraValue

Get the number of the data cube this extra value belongs to.

getDataCubeNo() - Method in class net.sf.basedb.core.DataCubeFilter

Get the number of the data cube this filter belongs to.

getDataCubeNo() - Method in class net.sf.basedb.core.DataCubeLayer

Get the number of the data cube this layer belongs to.

getDataCubeNo() - Method in class net.sf.basedb.core.ExtraValue

Get the number of the data cube the extra values are stored in.

getDataCubes() - Method in class net.sf.basedb.core.data.VirtualDbData

This is the inverse end.

getDataFile(DbControl, FileStoreEnabled, String, boolean) - Static method in class net.sf.basedb.core.FileStoreUtil

Get the file of the given data file type in the FileStoreEnabled item's file set assuming that at most one file exists.

getDataFile(TableInfo) - Method in class net.sf.basedb.core.Migration

Get the data file for the given table.

getDataFile(TableInfo, boolean) - Method in class net.sf.basedb.core.Migration

Get the data file for the given table.

getDataFileColumns(Item, String) - Static method in class net.sf.basedb.clients.web.Base

Get a query returning all data file types that are needed to display file set members for the given columns.

getDataFiles(DbControl, FileStoreEnabled, String, boolean) - Static method in class net.sf.basedb.core.FileStoreUtil

Get the file of the given data file type in the FileStoreEnabled item's file set.

getDataFileType() - Method in class net.sf.basedb.core.data.FileSetMemberData

Get the type of this file.

getDataFileType() - Method in class net.sf.basedb.core.data.FileTypeIndex

getDataFileType() - Method in class net.sf.basedb.core.data.ItemSubtypeFileTypeData

Get the file type.

getDataFileType() - Method in class net.sf.basedb.core.data.PlatformFileTypeData

Get the file type.

getDataFileType() - Method in class net.sf.basedb.core.FileSetMember

Get the type of the file.

getDataFileType() - Method in class net.sf.basedb.core.ItemSubtypeFileType

Get the type of the file.

getDataFileType() - Method in class net.sf.basedb.core.PlatformFileType

Get the type of the file.

getDataFileType() - Method in interface net.sf.basedb.core.UsableDataFileType

Get the data file type the information applies to.

getDataFileType() - Method in class net.sf.basedb.util.overview.Fix

getDataFileTypes() - Method in class net.sf.basedb.core.ItemSubtype

Get a query returning the data file types that have been associated with this subtype.

getDataFileTypes(Item, FileStoreEnabled, Platform, PlatformVariant, ItemSubtype) - Static method in class net.sf.basedb.clients.web.Base

Get a query that returns all data file types for a specific platform/variant/subtype that can be used on a given item type.

getDataSeparator() - Method in class net.sf.basedb.util.export.TableWriter

The data separator string is written between each data column in the output.

getDatatype() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

getDatatype() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn

getDataValue(Object) - Static method in class net.sf.basedb.core.Values

Convert an item values to a data value.

getDataValues(List<?>) - Static method in class net.sf.basedb.core.Values

Convert a list of item values to data values.

getDataWriterFactory() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter

Get the factory that creates data writers.

getDate() - Method in class net.sf.basedb.util.extensions.logging.LogEntry

The timestamp of the log entry as a date.

getDate(int, Formatter<Date>, boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser.Data

Get the value as a date.

getDate(int, Formatter<Date>, boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser.ExcelData

getDate(String[], Formatter<Date>) - Static method in class net.sf.basedb.util.Values

getDate(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.ColumnMapper

getDate(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.CompoundMapper

getDate(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.ConstantMapper

getDate(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.CropStringMapper

getDate(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.JepMapper

getDate(FlatFileParser.Data) - Method in interface net.sf.basedb.util.parser.Mapper

Get the value for the line of data as a date.

getDate(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.NullIfExceptionMapper

getDate(HttpResponse, String, Date) - Static method in class net.sf.basedb.util.HttpUtil

getDateCellStyle(String) - Method in class net.sf.basedb.util.excel.CellStyleCreator

Get the cell style for the given date format string.

getDateFormat() - Method in class net.sf.basedb.util.excel.AutoFormatter

getDateFormat() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil

Get the date formatter that is used for formatting cells with date-like values.

getDateFormat() - Method in class net.sf.basedb.util.formatter.DateFormatter

Get access to the underlying DateFormat object used for formatting and parsing dates.

getDateFormat(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterSettings

Get format string for a date formatter.

getDateFormatter(String) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

getDateFormatter(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory

Get the logged in user's date formatter.

getDateMapper(String) - Method in class net.sf.basedb.util.parser.FlatFileParser

Get a mapper using the default date format.

getDateTimeFormat(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterSettings

Get format string for a datetime formatter.

getDateTimeFormatter(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory

Get the logged in user's datetime formatter.

getDateValues() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink

getDbcontrol() - Method in class net.sf.basedb.clients.web.taglib.PropertyValue

getDbControl() - Method in class net.sf.basedb.core.AbstractBatcher

Get the DbControl object that currently manages this batcher.

getDbControl() - Method in class net.sf.basedb.core.BasicItem

Get the DbControl object that currently manages this item.

getDbControl() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

Get the current DbControl.

getDbControl() - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter

Get the DbControl to use for database access.

getDbControl() - Method in class net.sf.basedb.util.extensions.ClientContext

Get the current DbControl.

getDbControl() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter

Get the current DbControl.

getDbControl() - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter

Get the current DbControl.

getDbControl() - Method in class net.sf.basedb.util.listable.TransformContext

Get the DbControl to use in this transformation context.

getDbControl() - Method in class net.sf.basedb.util.units.UnitCache

Get the DbControl that is currently used for database access.

getDbEngine() - Static method in class net.sf.basedb.core.HibernateUtil

Get the database engine.

getDc() - Method in class net.sf.basedb.clients.web.taglib.SubtypeSelector

getDecimalSeparator() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

Get the decimal separator used by numbers in the file.

getDecimalSeparator() - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter

getDefault() - Method in class net.sf.basedb.core.Presets

Get the default preset.

getDefaultAnnotation() - Method in class net.sf.basedb.core.Annotation

Get the default annotation that this project-specific annotation is overriding.

getDefaultClazz(int) - Method in class net.sf.basedb.clients.web.taglib.Body

getDefaultDateFormat() - Method in class net.sf.basedb.util.parser.FlatFileParser

Get the default date format.

getDefaultErrorHandlerFactory() - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Get the default error handling factory.

getDefaultErrorHandlerFactory() - Method in class net.sf.basedb.util.extensions.Registry

Get the default error handler factory.

getDefaultFileExtension() - Method in interface net.sf.basedb.clients.web.plugins.ExportTemplate

Get the default file extension to give to files generated by this template.

getDefaultFileExtension() - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate

getDefaultFileExtension() - Method in class net.sf.basedb.clients.web.plugins.XlsxTemplate

getDefaultFileExtension() - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate

getDefaultId(String) - Method in class net.sf.basedb.clients.web.taglib.Button

getDefaultImage(String) - Method in class net.sf.basedb.clients.web.taglib.Button

getDefaultItemFunction(Item) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Create a DefaultItemFunction for the given item type.

getDefaultItems() - Method in class net.sf.basedb.core.data.ProjectData

The default items to use in this project

getDefaultItems(DbControl) - Method in class net.sf.basedb.core.Project

Get a list with all default items added to this project.

getDefaultItems(DbControl, Item) - Method in class net.sf.basedb.core.Project

Get a list with all default items of a given item type added to this project.

getDefaultKeyManagers() - Static method in class net.sf.basedb.util.ssl.SSLUtil2

Get the default keys manages as configured in the base.config file by ssl.keystore.* settings.

getDefaultNumberFormat() - Method in class net.sf.basedb.util.parser.FlatFileParser

Get the default number format.

getDefaultPriority() - Method in enum class net.sf.basedb.core.Job.ExecutionTime

The default thread priority to use when executing jobs in with this execution time.

getDefaultRawDataType() - Method in class net.sf.basedb.core.Project

Gets the default raw data type for this project.

getDefaultRememberDevice() - Method in class net.sf.basedb.core.SessionControl.UnverifiedDeviceInfo

The preferred setting for the "rememberDevice" parameter when verifying the device.

getDefaultReporterContext() - Method in class net.sf.basedb.clients.web.ExperimentExplorer

Get the default reporter context that is used to initialise the actual context.

getDefaultSelects() - Method in class net.sf.basedb.core.AbstractSqlQuery

getDefaultSelects() - Method in class net.sf.basedb.core.DataCube.RawMappingQuery

getDefaultSelects() - Method in class net.sf.basedb.core.DynamicExtraValueQuery

Default selection: column, position, extraValue

getDefaultSelects() - Method in class net.sf.basedb.core.DynamicPositionQuery

Default selection: position

getDefaultSelects() - Method in class net.sf.basedb.core.DynamicRawDataQuery

No default selection.

getDefaultSelects() - Method in class net.sf.basedb.core.DynamicReporterQuery

No default selection.

getDefaultSelects() - Method in class net.sf.basedb.core.DynamicSpotQuery

Default selection: column, postion, ch1, ch2, ...

getDefaultSetting(String) - Method in class net.sf.basedb.core.Client

Get the default setting with the specified name.

getDefaultSettings() - Method in class net.sf.basedb.core.Client

Get a query that will return all default settings for this client.

getDefaultSettings() - Method in class net.sf.basedb.core.data.ClientData

This is the inverse end.

getDefaultSettings() - Method in class net.sf.basedb.core.data.UserData

This is the inverse end.

getDefaultSettings() - Method in class net.sf.basedb.core.User

Get a query that returns all default settings for this user.

getDefaultSeverity() - Method in interface net.sf.basedb.util.overview.extensions.ValidationRuleAction

Get the default severity level.

getDefaultSeverity() - Method in class net.sf.basedb.util.overview.Validator

Get the default severity level.

getDefaultSlots() - Method in enum class net.sf.basedb.core.Job.ExecutionTime

The default number of execution slots available for jobs with this execution time in the internal job queue.

getDefaultSpotContext() - Method in class net.sf.basedb.clients.web.ExperimentExplorer

Get the default spot context that is used to initialise the actual context.

getDefaultSystemId(Item) - Static method in class net.sf.basedb.core.Hardware

Get the system id for the hardware subtype that should be used on an item that doesn't have a subtype.

getDefaultSystemId(Item) - Static method in class net.sf.basedb.core.Kit

Get the system id for the kit subtype that should be used on an item that doesn't have a subtype.

getDefaultSystemId(Item) - Static method in class net.sf.basedb.core.Protocol

Get the system id for the protocol subtype that should be used on an item that doesn't have a subtype.

getDefaultSystemId(Item) - Static method in class net.sf.basedb.core.Software

Get the system id for the software subtype that should be used on an item that doesn't have a subtype.

getDefaultTimestampFormat() - Method in class net.sf.basedb.util.parser.FlatFileParser

Get the default timestamp format.

getDefaultTransactionName(String) - Method in class net.sf.basedb.core.SessionControl

Generate a default transaction name with an optional suffix.

getDefaultTrustManagers() - Static method in class net.sf.basedb.util.ssl.SSLUtil2

Get the default trust manages as configured in the base.config file by ssl.truststore.* settings.

getDefaultUnit() - Method in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo

Get the default unit for the annotation type.

getDefaultUnit() - Method in class net.sf.basedb.core.AnnotationType

Get the default unit for this annotation type.

getDefaultUnit() - Method in class net.sf.basedb.core.data.AnnotationTypeData

Get the unit used to store annotation values for this type.

getDefaultValue() - Method in class net.sf.basedb.core.AnnotationType

Get the recommended default value for new annotations of this annotation type.

getDefaultValue() - Method in class net.sf.basedb.core.data.AnnotationTypeData

The default value of new annotations.

getDefaultValue() - Method in class net.sf.basedb.core.ParameterType

Get the default value.

getDefaultValue() - Method in class net.sf.basedb.core.PluginParameter

Get the default value for this parameter or null if no default has been specified

getDefaultValue() - Method in class net.sf.basedb.core.query.ParameterExpression

Get the default value of the parameter.

getDefaultValue() - Method in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter

getDefaultValue() - Method in class net.sf.basedb.plugins.executor.ParameterDefinition

Get the default value for this parameter.

getDefaultValue() - Method in class net.sf.basedb.util.formatter.LookupFormatter

Get the default value.

getDefinedPermissions() - Method in enum class net.sf.basedb.core.Item

Get the permissions which are meaningful to assign to an item if this type.

getDelegate() - Method in class net.sf.basedb.core.hibernate.SessionWrapper

getDelegateFirst() - Method in class net.sf.basedb.util.JarClassLoader

If this class loader delegates to the parent class loader before or after trying to find the class by itself.

getDeletePropertyOrder(Class<? extends BatchableData>) - Static method in class net.sf.basedb.core.BatchUtil

Get the order of properties in the delete SQL.

getDeletePropertyOrder(String) - Static method in class net.sf.basedb.core.BatchUtil

Get the order of properties in the delete SQL.

getDeleteSql(Class<? extends BatchableData>) - Static method in class net.sf.basedb.core.BatchUtil

Get the SQL that deletes a new row of the specified class.

getDeleteSql(String) - Static method in class net.sf.basedb.core.BatchUtil

Get the SQL that deletes a new row of the specified class.

getDeletionOrder() - Method in enum class net.sf.basedb.core.Item

Get a value indicating the deletion order.

getDenied() - Method in class net.sf.basedb.core.data.keyring.PluginKeys

Get the denied permissions.

getDenied() - Method in class net.sf.basedb.core.data.PluginPermission

The plugin's permission can be set to always be used or only if the user has it already.

getDenied(RoleKey) - Method in class net.sf.basedb.core.PluginDefinition

Get the permissions that have been denied to this plugin.

getDeniedItemFix(DbControl, Node, Node) - Method in class net.sf.basedb.util.overview.validator.BasicNodeValidator

Subclasses should override this method if they have a suggessted fix for an access denied problem.

getDeniedNodeName(Node) - Method in class net.sf.basedb.util.overview.node.AnnotationNameGenerator

getDeniedNodeName(Node) - Method in class net.sf.basedb.util.overview.node.AnyToAnyNameGenerator

getDeniedNodeName(Node) - Method in class net.sf.basedb.util.overview.node.BioWellNameGenerator

getDeniedNodeName(Node) - Method in class net.sf.basedb.util.overview.node.FileSetMemberNameGenerator

getDeniedNodeName(Node) - Method in class net.sf.basedb.util.overview.node.ItemListMemberNameGenerator

getDeniedNodeName(Node) - Method in class net.sf.basedb.util.overview.node.NameableNameGenerator

getDeniedNodeName(Node) - Method in interface net.sf.basedb.util.overview.node.NodeNameGenerator

Generate a name for a node when the item exists, but the current user doesn't have permission to access read the item.

getDeniedNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.AnnotationNameGenerator

getDeniedNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.AnyToAnyNameGenerator

getDeniedNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.BioWellNameGenerator

getDeniedNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.FileSetMemberNameGenerator

getDeniedNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.ItemListMemberNameGenerator

getDeniedNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.NameableNameGenerator

getDeniedNodeTitle(Node) - Method in interface net.sf.basedb.util.overview.node.NodeNameGenerator

Generate a title for a node when the item exists, but the current user doesn't have permission to access read the item.

getDependingLists() - Method in class net.sf.basedb.core.ItemList

Get a query that return all item lists that are used by synchronization filters in this list.

getDepth() - Method in class net.sf.basedb.util.Tree.Entry

Get the depth of this entry within the tree.

getDerivedBioAssays() - Method in class net.sf.basedb.core.data.ExtractData

This is the inverse end.

getDerivedBioAssays() - Method in class net.sf.basedb.core.data.JobData

This is the inverse end.

getDerivedBioAssays() - Method in class net.sf.basedb.core.data.PhysicalBioAssayData

This is the inverse end.

getDerivedBioAssays() - Method in class net.sf.basedb.core.Extract

Get a query that returns all derived bioassays created from this extract.

getDerivedBioAssays() - Method in class net.sf.basedb.core.PhysicalBioAssay

Get a query that returns all derived bioassay created from this physical bioassay.

getDescription() - Method in class net.sf.basedb.clients.jobagent.Agent

Get the agent.description configuration value.

getDescription() - Method in interface net.sf.basedb.clients.web.extensions.plot.OverviewPlotAction

A description of the overview plots.

getDescription() - Method in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean

getDescription() - Method in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory

getDescription() - Method in interface net.sf.basedb.clients.web.extensions.startpage.StartPageAction

Get an optional description of the start page.

getDescription() - Method in class net.sf.basedb.clients.web.extensions.startpage.StartPageBean

getDescription() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn

getDescription() - Method in class net.sf.basedb.core.AnyToAny

getDescription() - Method in class net.sf.basedb.core.authentication.ExtraUserInformation

A description of the user.

getDescription() - Method in class net.sf.basedb.core.BioAssay

getDescription() - Method in class net.sf.basedb.core.BioAssaySet

getDescription() - Method in class net.sf.basedb.core.BioPlateEventType

getDescription() - Method in class net.sf.basedb.core.BioPlateType

getDescription() - Method in class net.sf.basedb.core.CommonItem

getDescription() - Method in class net.sf.basedb.core.data.AnyToAnyData

getDescription() - Method in class net.sf.basedb.core.data.BioAssayData

getDescription() - Method in class net.sf.basedb.core.data.BioAssaySetData

getDescription() - Method in class net.sf.basedb.core.data.BioPlateEventTypeData

getDescription() - Method in class net.sf.basedb.core.data.BioPlateTypeData

getDescription() - Method in class net.sf.basedb.core.data.CommonData

getDescription() - Method in class net.sf.basedb.core.data.DataFileTypeData

getDescription() - Method in class net.sf.basedb.core.data.ExtraValueTypeData

getDescription() - Method in class net.sf.basedb.core.data.GroupData

getDescription() - Method in class net.sf.basedb.core.data.HelpData

getDescription() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData

getDescription() - Method in class net.sf.basedb.core.data.ItemSubtypeData

getDescription() - Method in class net.sf.basedb.core.data.MessageData

getDescription() - Method in class net.sf.basedb.core.data.MimeTypeData

getDescription() - Method in interface net.sf.basedb.core.data.NameableData

Get the description for the item.

getDescription() - Method in class net.sf.basedb.core.data.NewsData

getDescription() - Method in class net.sf.basedb.core.data.ParameterValueData

Get the description of the parameter.

getDescription() - Method in class net.sf.basedb.core.data.PlateEventTypeData

getDescription() - Method in class net.sf.basedb.core.data.PlateGeometryData

getDescription() - Method in class net.sf.basedb.core.data.PlatformData

getDescription() - Method in class net.sf.basedb.core.data.PlatformVariantData

getDescription() - Method in class net.sf.basedb.core.data.PluginDefinitionData

Get a description of the plugin.

getDescription() - Method in class net.sf.basedb.core.data.PluginTypeData

getDescription() - Method in class net.sf.basedb.core.data.ProjectData

getDescription() - Method in class net.sf.basedb.core.data.QuantityData

getDescription() - Method in class net.sf.basedb.core.data.QuotaData

getDescription() - Method in class net.sf.basedb.core.data.QuotaTypeData

getDescription() - Method in class net.sf.basedb.core.data.ReporterClonePropertyData

Get a description of the property.

getDescription() - Method in class net.sf.basedb.core.data.ReporterData

getDescription() - Method in class net.sf.basedb.core.data.ReporterTypeData

getDescription() - Method in class net.sf.basedb.core.data.RoleData

getDescription() - Method in class net.sf.basedb.core.data.RoleKeyData

Get the description for the item.

getDescription() - Method in class net.sf.basedb.core.data.RootRawBioAssayData

getDescription() - Method in class net.sf.basedb.core.data.TransformationData

getDescription() - Method in class net.sf.basedb.core.data.UnitData

getDescription() - Method in class net.sf.basedb.core.data.UserData

getDescription() - Method in class net.sf.basedb.core.data.UserDeviceData

getDescription() - Method in class net.sf.basedb.core.DataFileType

getDescription() - Method in class net.sf.basedb.core.Directory

getDescription() - Method in class net.sf.basedb.core.ExtendedProperty

Get a description of the extended property.

getDescription() - Method in class net.sf.basedb.core.ExtraValueType

getDescription() - Method in class net.sf.basedb.core.Group

getDescription() - Method in class net.sf.basedb.core.Help

getDescription() - Method in class net.sf.basedb.core.IntensityFormula

Get a description of the intensity formula.

getDescription() - Method in class net.sf.basedb.core.ItemSubtype

getDescription() - Method in class net.sf.basedb.core.Message

getDescription() - Method in class net.sf.basedb.core.MimeType

getDescription() - Method in interface net.sf.basedb.core.Nameable

Get the description for the item.

getDescription() - Method in class net.sf.basedb.core.News

getDescription() - Method in class net.sf.basedb.core.ParameterInfo

getDescription() - Method in class net.sf.basedb.core.PlateEventType

getDescription() - Method in class net.sf.basedb.core.PlateGeometry

getDescription() - Method in class net.sf.basedb.core.Platform

getDescription() - Method in class net.sf.basedb.core.PlatformVariant

getDescription() - Method in interface net.sf.basedb.core.plugin.About

A description of the plugin and what it does.

getDescription() - Method in class net.sf.basedb.core.plugin.AboutImpl

getDescription() - Method in class net.sf.basedb.core.PluginParameter

Get a description of the parameter.

getDescription() - Method in class net.sf.basedb.core.PluginType

getDescription() - Method in class net.sf.basedb.core.Project

getDescription() - Method in class net.sf.basedb.core.Quantity

getDescription() - Method in class net.sf.basedb.core.Quota

getDescription() - Method in class net.sf.basedb.core.QuotaType

getDescription() - Method in class net.sf.basedb.core.RawDataType

Get a description of this raw data type.

getDescription() - Method in class net.sf.basedb.core.ReporterType

getDescription() - Method in class net.sf.basedb.core.RequestInformation

Get a description of the request.

getDescription() - Method in class net.sf.basedb.core.Role

getDescription() - Method in class net.sf.basedb.core.RoleKey

getDescription() - Method in class net.sf.basedb.core.RootRawBioAssay

getDescription() - Method in class net.sf.basedb.core.signal.Signal

Get the description of the what the signal means and how receivers should behave when the signal is sent to them

getDescription() - Method in class net.sf.basedb.core.SyncFilter

getDescription() - Method in class net.sf.basedb.core.Transformation

getDescription() - Method in class net.sf.basedb.core.Unit

getDescription() - Method in class net.sf.basedb.core.User

getDescription() - Method in class net.sf.basedb.core.UserDevice

getDescription() - Method in class net.sf.basedb.plugins.executor.ParameterDefinition

Get a description/help text about this parameter.

getDescription() - Method in class net.sf.basedb.util.extensions.AboutBean

getDescription() - Method in interface net.sf.basedb.util.extensions.ExtensionPoint

Get a description of the extension point.

getDescription() - Method in class net.sf.basedb.util.extensions.ExtensionPointBean

getDescription() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout

getDescription() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint

getDescription() - Method in class net.sf.basedb.util.jep.convert.AbsConverter

getDescription() - Method in class net.sf.basedb.util.jep.convert.AbstractJepConversionFunction

getDescription() - Method in class net.sf.basedb.util.jep.convert.AddConverter

getDescription() - Method in class net.sf.basedb.util.jep.convert.AndConverter

getDescription() - Method in class net.sf.basedb.util.jep.convert.DivideConverter

getDescription() - Method in class net.sf.basedb.util.jep.convert.EqualsConverter

getDescription() - Method in class net.sf.basedb.util.jep.convert.ExpConverter

getDescription() - Method in class net.sf.basedb.util.jep.convert.GreaterConverter

getDescription() - Method in class net.sf.basedb.util.jep.convert.GreaterEqualsConverter

getDescription() - Method in class net.sf.basedb.util.jep.convert.IfConverter

getDescription() - Method in interface net.sf.basedb.util.jep.convert.JepConversionFunction

Get a short description of the function or operator

getDescription() - Method in class net.sf.basedb.util.jep.convert.LessConverter

getDescription() - Method in class net.sf.basedb.util.jep.convert.LessEqualsConverter

getDescription() - Method in class net.sf.basedb.util.jep.convert.LogarithmConverter

getDescription() - Method in class net.sf.basedb.util.jep.convert.MultiplyConverter

getDescription() - Method in class net.sf.basedb.util.jep.convert.NaturalLogarithmConverter

getDescription() - Method in class net.sf.basedb.util.jep.convert.NotConverter

getDescription() - Method in class net.sf.basedb.util.jep.convert.NotEqualsConverter

getDescription() - Method in class net.sf.basedb.util.jep.convert.OrConverter

getDescription() - Method in class net.sf.basedb.util.jep.convert.SquareRootConverter

getDescription() - Method in class net.sf.basedb.util.jep.convert.SubtractConverter

getDescription() - Method in class net.sf.basedb.util.jep.convert.UMinusConverter

getDescription() - Method in interface net.sf.basedb.util.overview.extensions.ValidationRuleAction

Get a lengthier description of the validation that takes place

getDescription() - Method in class net.sf.basedb.util.overview.Validator

Get a lengthier description of the validation that takes place

getDescription() - Method in interface net.sf.basedb.util.uri.ConnectionManagerFactory

Get a longer description that can be used by client applications to show more information about the capabilities of the factory to the users.

getDescription() - Method in class net.sf.basedb.util.uri.http.HttpConnectionManagerFactory

getDescription() - Method in class net.sf.basedb.util.zip.Bzip2FilePacker

getDescription() - Method in interface net.sf.basedb.util.zip.FilePacker

Get a short description of this file format that is suitable for display in selection list boxes.

getDescription() - Method in class net.sf.basedb.util.zip.GzipFilePacker

getDescription() - Method in class net.sf.basedb.util.zip.TarFilePacker

getDescription() - Method in class net.sf.basedb.util.zip.ZipFilePacker

getDescriptor() - Method in class net.sf.basedb.util.overview.Failure

getDestinationCount() - Method in class net.sf.basedb.core.data.PlateMappingData

The produced number of destination plates.

getDestinationCount() - Method in class net.sf.basedb.core.PlateMapping

Get the number of produced destination plates.

getDestinationGeometry() - Method in class net.sf.basedb.core.data.PlateMappingData

The required geometry of destination plates in this mapping.

getDestinationGeometry() - Method in class net.sf.basedb.core.PlateMapping

Get the PlateGeometry of the created plates.

getDestinationIndex() - Method in class net.sf.basedb.core.data.PlateData

If the plate was created by a plate mapping, this is the index of this plate in the list of created plates.

getDestinationIndex() - Method in class net.sf.basedb.core.Plate

If the plate was created by a plate mapping, this is the index of this plate in the list of created plates.

getDetail() - Method in exception net.sf.basedb.clients.web.WebException

Get the detailed description of the error message.

getDetails() - Method in class net.sf.basedb.core.data.ChangeHistoryData

This is the inverse end.

getDetails() - Method in class net.sf.basedb.core.data.PlateMappingData

For each destination coordinate we can get the source coordinate.

getDevice() - Method in class net.sf.basedb.core.data.SessionData

Get the device the user was using.

getDevice() - Method in class net.sf.basedb.core.Session

Get the device the user was using in this session.

getDeviceId() - Method in class net.sf.basedb.core.SessionControl

Get the id of the UserDevice in use.

getDeviceName() - Method in class net.sf.basedb.core.SessionControl

Get the name of the UserDevice in use.

getDevices() - Method in class net.sf.basedb.core.data.ClientData

This is the inverse end.

getDevices() - Method in class net.sf.basedb.core.data.UserData

This is the inverse end.

getDeviceToken() - Method in class net.sf.basedb.core.authentication.LoginRequest

Get the deviceToken to use.

getDeviceToken() - Method in class net.sf.basedb.core.SessionControl.UnverifiedDeviceInfo

Get the token for this device.

getDialect() - Static method in class net.sf.basedb.core.HibernateUtil

Get the database dialect.

getDifference() - Method in interface net.sf.basedb.core.DiskConsumable

Get the number of bytes this items now is using compared to when it was loaded from the database.

getDifference() - Method in class net.sf.basedb.core.Experiment

getDifference() - Method in class net.sf.basedb.core.File

Always 0.

getDifference() - Method in class net.sf.basedb.core.RawBioAssay

Always 0.

getDirection() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

Get the parsed value of the DIRECTION.

getDirection() - Method in class net.sf.basedb.clients.web.taglib.table.Table

getDirectionImage(ItemContext.SortDirection) - Method in class net.sf.basedb.clients.web.taglib.table.Table

Get sort direction <img> element for the given direction.

getDirectionRaw() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

Get the raw value of the DIRECTION.

getDirectory() - Method in class net.sf.basedb.core.data.ExperimentData

Get the associated DirectoryData item directory where it is recommended for plugins to save files related to the experiment.

getDirectory() - Method in class net.sf.basedb.core.data.FileData

Get the associated DirectoryData item.

getDirectory() - Method in class net.sf.basedb.core.Experiment

Get the associated directory where it is recommended that plugins store files that are related to this experiment.

getDirectory() - Method in class net.sf.basedb.core.File

Get the associated Directory item.

getDirectory(int) - Method in class net.sf.basedb.core.Path

Get the name of the i:th directory on the path, starting with 0.

getDirectory(DbControl, Path) - Method in class net.sf.basedb.plugins.batchimport.FileImporter

getDirectory(DbControl, Path) - Method in class net.sf.basedb.plugins.TarFileUnpacker

Get the directory for the specified path.

getDirectory(Path) - Method in class net.sf.basedb.util.zip.ZipUnpacker

Get the directory for the specified path.

getDirectoryCount() - Method in class net.sf.basedb.core.Path

Get the number of directories on the path.

getDirectoryParameter(String, String) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker

Get a plugin parameter that asks for the directory where the unpacked files are stored.

getDirectoryTree(DbControl, Directory) - Static method in class net.sf.basedb.util.FileUtil

Get the complete tree of sub-directories from a given directory.

getDirty(int) - Method in class net.sf.basedb.core.log.EntityDetails

getDisableInheritance() - Method in class net.sf.basedb.core.AnnotationType

If this flag is set, annotations of this type can't be inherited to child items.

getDisableInheritance() - Method in class net.sf.basedb.core.data.AnnotationTypeData

If this flag is set, annotation of this type can't be inherited.

getDisableinproject() - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector

getDisableLogOfValues() - Method in class net.sf.basedb.core.AnnotationType

If this flag is set, the change history logging will not include actual annotation values.

getDisableLogOfValues() - Method in class net.sf.basedb.core.data.AnnotationTypeData

If this flag is set, logging of actual annotation values should not be done in the change history.

getDisableManualMembers() - Method in class net.sf.basedb.core.data.ItemListData

If set, manually adding/removing members is disabled

getDisableManualMembers() - Method in class net.sf.basedb.core.ItemList

If this flag is set manual modification of members is disabled.

getDisableothers() - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector

getDisableOverflowCheck() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

getDisableOverflowCheck() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction

If set, text overflow check is disabled for this column.

getDisableownedby() - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector

getDisableRawJoinOnMergedData() - Method in class net.sf.basedb.core.DynamicSpotQuery

getDisableremoved() - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector

getDisablesharedto() - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector

getDisableSyncFilters() - Method in class net.sf.basedb.core.data.ItemListData

If set, syncing members with sync filter is disabled

getDisableSyncFilters() - Method in class net.sf.basedb.core.ItemList

If this flag is set synchronization of members with sync filters is disabled.

getDiskConsumableItems() - Static method in class net.sf.basedb.core.Metadata

Get a set containing all DiskConsumable item types.

getDiskUsage() - Method in interface net.sf.basedb.core.data.DiskConsumableData

Get the DiskUsageData that this item use.

getDiskUsage() - Method in class net.sf.basedb.core.data.ExperimentData

getDiskUsage() - Method in class net.sf.basedb.core.data.FileData

getDiskUsage() - Method in class net.sf.basedb.core.data.RawBioAssayData

getDiskUsage(GroupData, QuotaTypeData, Location) - Method in class net.sf.basedb.core.DbControl

Get the disk usage for the specified group at the specified location and quota type.

getDiskUsage(UserData, QuotaTypeData, Location) - Method in class net.sf.basedb.core.DbControl

Get the disk usage for the specified user at the specified location and quota type.

getDiskUsage(QuotaType, Location) - Method in class net.sf.basedb.core.Group

Get the used number of bytes for the specified quota type and location.

getDiskUsage(QuotaType, Location) - Method in class net.sf.basedb.core.User

Get the used number of bytes for the specified quota type and location.

getDisplayAsList() - Method in class net.sf.basedb.core.AnnotationType

Check if the enumeration values should be displayed as a selection list or as radio buttons/checkboxes by the client application.

getDisplayName() - Method in interface net.sf.basedb.clients.web.extensions.login.LoginFormAction

Get a name that can be displayed for users in a selection list or similar to switch between different login methods.

getDisplayName() - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean

getDisplayName() - Method in class net.sf.basedb.clients.web.extensions.login.PasswordLoginFormFactory

getDisplayName() - Method in interface net.sf.basedb.util.uri.ConnectionManagerFactory

Get a short string that is suitable for use in selection lists, etc.

getDisplayName() - Method in class net.sf.basedb.util.uri.http.HttpConnectionManagerFactory

getDisplaySymbol() - Method in class net.sf.basedb.core.data.UnitData

The symbol to display together with values of this unit.

getDisplaySymbol() - Method in class net.sf.basedb.core.Unit

Get the display symbol to use when displaying values with this unit.

getDoctype() - Method in class net.sf.basedb.clients.web.taglib.Page

getDomainOrder() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset

getDouble(int, NumberFormat, boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser.Data

Get the value as a double.

getDouble(int, NumberFormat, boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser.ExcelData

getDouble(String) - Static method in class net.sf.basedb.util.Values

Convert a string to a double.

getDouble(String[]) - Static method in class net.sf.basedb.util.Values

Convert an array of strings to an array of Double:s.

getDouble(String, double) - Static method in class net.sf.basedb.util.Values

Convert a string to a double.

getDouble(String, Double) - Static method in class net.sf.basedb.util.Values

getDouble(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.ColumnMapper

getDouble(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.CompoundMapper

getDouble(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.ConstantMapper

getDouble(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.CropStringMapper

getDouble(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.JepMapper

getDouble(FlatFileParser.Data) - Method in interface net.sf.basedb.util.parser.Mapper

Get the value for the line of data as a double.

getDouble(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.NullIfExceptionMapper

getDoubleFormatter(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory

Get the logged in user's number formatter for double values.

getDoubleOption(String, Double) - Method in class net.sf.basedb.core.AnnotationType

Get an option and convert the value to a double.

getDoubleValues() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink

getDownloadStream(long) - Method in class net.sf.basedb.core.File

Get an InputStream that can be used to download the physical file for this file item.

getDragcolumns() - Method in class net.sf.basedb.clients.web.taglib.table.Table

getDropForeignKeySql(String, String, String, String) - Method in interface net.sf.basedb.core.dbengine.DbEngine

Generate SQL to drop a foreign key constraint.

getDropForeignKeySql(String, String, String, String) - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine

Generate alter table <catalog>.<schema>.<table> drop constraint <name>

getDropForeignKeySql(String, String, String, String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine

Generate alter table <catalog>.<table> drop foreign key <name>

getDropForeignKeySql(String, String, String, String) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine

Generate alter table <schema>.<table> DROP CONSTRAINT <name>

getDropIndexSql(String, String, String, String, boolean) - Method in interface net.sf.basedb.core.dbengine.DbEngine

Generate SQL to drop an index.

getDropIndexSql(String, String, String, String, boolean) - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine

Generate drop index <catalog>.<schema>.<table>.<name>.

getDropIndexSql(String, String, String, String, boolean) - Method in class net.sf.basedb.core.dbengine.MySQLEngine

Generate drop index <name> on <catalog>.<table>.

getDropIndexSql(String, String, String, String, boolean) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine

Generate alter table <schema>.<table> drop constraint <name> for unique indexes, drop index <schema>.<name> for other indexes.

getDropPrimaryKey(String, String, String, String) - Method in interface net.sf.basedb.core.dbengine.DbEngine

Generate SQL that drops the primary key from a table.

getDropPrimaryKey(String, String, String, String) - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine

getDropPrimaryKey(String, String, String, String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine

Generate alter table catalog.table drop primary key

getDropPrimaryKey(String, String, String, String) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine

Generate alter table schema.table drop constraint name

getDynamicActionAttributes() - Method in class net.sf.basedb.clients.web.extensions.AbstractJspFactory

getDynamicActionAttributes() - Method in interface net.sf.basedb.clients.web.extensions.DynamicActionAttributes

Get an iterator that return all dynamic attributes.

getDynamicActionAttributes() - Method in class net.sf.basedb.clients.web.extensions.DynamicActionAttributeSupport

getDynamicActionAttributes() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction

Get extra attributes that will be outputted in the HTML for the list column.

getDynamicActionAttributes() - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory.MySkinAction

getDynamicActionAttributes() - Method in class net.sf.basedb.clients.web.taglib.StylableTag

getDynamicActionAttributes() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab

getDynamicActionAttributes() - Method in class net.sf.basedb.clients.web.taglib.table.Button.ButtonActionWrapper

getDynamicAttribute(String) - Method in class net.sf.basedb.clients.web.taglib.StylableTag

Get the dynamic attribute for the given name

getDynamicCatalog() - Static method in class net.sf.basedb.core.Application

Get the name of the dynamic catalog.

getDynamicExpression(DbControl, SqlQuery, String) - Static method in class net.sf.basedb.core.ItemContext

Create an Expression from a string.

getDynamicQuery() - Static method in class net.sf.basedb.core.Reporter

Get a dynamic query object configured to retrieve reporter information.

getDynamicQuery(Experiment) - Static method in class net.sf.basedb.core.Reporter

Get a dynamic query object configured to retrieve reporter information from either the master reporter table or a cloned reporter table in the given experiment.

getDynamicRawData() - Method in class net.sf.basedb.core.RawBioAssay

Get a dynamic query that returns the raw data of this raw bioassay.

getDynamicRestriction(DbControl, SqlQuery) - Method in class net.sf.basedb.core.PropertyFilter

getDynamicSchema() - Static method in class net.sf.basedb.core.Application

Get the name of the dynamic schema.

getDynamicSelect(DbControl, SqlQuery, String) - Static method in class net.sf.basedb.core.ItemContext

Same as ItemContext.getDynamicExpression(DbControl, SqlQuery, String) but generates a select object instead.

getEffectiveFilter() - Method in class net.sf.basedb.core.ItemContext.PropertyFilterPair

getEffectiveMaxMemory() - Method in class net.sf.basedb.core.JobAgentSettings

Get the effective maximum amount of memory the plugin is allowed to use.

getEffectivePriority(Job) - Method in class net.sf.basedb.core.JobAgentSettings

Get the effective priority for the specified job, when the priority boost is taken into account.

getElementClass() - Method in class net.sf.basedb.core.DynamicPositionQueryJoiners.ExtraValueJoiner

getElementClass() - Method in class net.sf.basedb.core.DynamicPositionQueryJoiners.ReporterJoiner

getElementClass() - Method in class net.sf.basedb.core.DynamicPositionQueryJoiners.ReporterListJoiner

getElementClass() - Method in class net.sf.basedb.core.DynamicRawDataQuery.RawBioAssayJoiner

getElementClass() - Method in class net.sf.basedb.core.DynamicRawDataQuery.ReporterJoiner

getElementClass() - Method in class net.sf.basedb.core.DynamicRawDataQuery.ReporterListJoiner

getElementClass() - Method in class net.sf.basedb.core.DynamicReporterQuery.MasterReporterJoiner

getElementClass() - Method in class net.sf.basedb.core.DynamicReporterQuery.ReporterListJoiner

getElementClass() - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.ExtraValueJoiner

getElementClass() - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.RawDataJoiner

getElementClass() - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.ReporterJoiner

getElementClass() - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.ReporterListJoiner

getElementClass() - Method in class net.sf.basedb.core.HqlQueryJoiners.AnnotationJoiner

getElementClass() - Method in class net.sf.basedb.core.HqlQueryJoiners.ReporterListJoiner

getElementClass() - Method in interface net.sf.basedb.core.query.AutoJoiner

The type of the query element the implementation works for.

getEmail() - Method in class net.sf.basedb.core.authentication.ExtraUserInformation

getEmail() - Method in class net.sf.basedb.core.data.PluginDefinitionData

Get an email address that can be used to get more information about the plugin.

getEmail() - Method in class net.sf.basedb.core.data.UserData

Get the email address to the user, or null if unknown.

getEmail() - Method in interface net.sf.basedb.core.plugin.About

An email adress to get more information about the plugin.

getEmail() - Method in class net.sf.basedb.core.plugin.AboutImpl

getEmail() - Method in class net.sf.basedb.core.PluginDefinition

Get an email address that can be used to get more information about the plugin.

getEmail() - Method in class net.sf.basedb.core.User

Get the email address to the user.

getEmail() - Method in class net.sf.basedb.util.extensions.AboutBean

getEmail() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout

getEnabledFilter(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

getEnabledItems() - Method in class net.sf.basedb.core.AnnotationType

Get the Item types this annotation type is enabled for.

getEnableDownloadLink() - Method in class net.sf.basedb.clients.web.taglib.PropertyValue

getEnableEditLink() - Method in class net.sf.basedb.clients.web.taglib.PropertyValue

getEnablePropertyLink() - Method in class net.sf.basedb.clients.web.taglib.PropertyValue

getEncodedName(Nameable, boolean) - Static method in class net.sf.basedb.clients.web.Base

Encode the name of the nameable item using the HTML.encodeTags(String) method.

getEncoder() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil

Get the current encoder.

getEncoder() - Method in class net.sf.basedb.util.export.TableWriter

Get the current default encoder for this writer.

getEndDate() - Method in class net.sf.basedb.core.data.NewsData

Get the last day this news item should be shown.

getEndDate() - Method in class net.sf.basedb.core.News

Get the end date and time for this news item to be published.

getEnded() - Method in class net.sf.basedb.core.data.JobData

Get the date and time the job was ended or null if the job hasn't ended.

getEnded() - Method in class net.sf.basedb.core.Job

Get the date and time the job ended.

getEndTime() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults

Get the end time of the scan as a millisecond value.

getEndX() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin

getEndX(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset

getEndXValue(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset

getEndY(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset

getEndYValue(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset

getEntity() - Method in class net.sf.basedb.core.log.EntityDetails

Get the entity that was changed.

getEntityGraph(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

getEntityGraphs(Class<T>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

getEntityLogger(LogManager, Object) - Method in class net.sf.basedb.core.log.db.DbLogManagerFactory

If a special logger has been registered for the class of the given entity, use that logger, otherwise use the default logger.

getEntityLogger(LogManager, Object) - Method in interface net.sf.basedb.core.log.LogManagerFactory

Get/create an entity logger for logging changes to the given entity.

getEntityLogOptions(Object) - Static method in class net.sf.basedb.core.log.EntityLogOptions

Get the logging options for the given entity.

getEntityLogOptionsForClass(Class<?>) - Static method in class net.sf.basedb.core.log.EntityLogOptions

Get the logging options for the given class of entities.

getEntityManagerFactory() - Method in class net.sf.basedb.core.hibernate.SessionWrapper

getEntityName() - Method in class net.sf.basedb.core.RawDataType

getEntityName(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

getEntriesByKey(K) - Method in class net.sf.basedb.util.Enumeration

Get a list with all entries that equals the given key.

getEntriesByValue(V) - Method in class net.sf.basedb.util.Enumeration

Get a list with all entries that equals the given value.

getEntry(int) - Method in class net.sf.basedb.util.bfs.MetadataModel.Section

Get the entry in this section with the given index.

getEntry(int) - Method in class net.sf.basedb.util.Enumeration

getEntry(E) - Method in class net.sf.basedb.util.Tree

Get the entry for an arbitrary node.

getEntry(String) - Method in class net.sf.basedb.util.bfs.MetadataModel.Section

Get the first entry in this section with a given key.

getEntryCount() - Method in class net.sf.basedb.util.bfs.MetadataModel.Section

Get the number of entries in this section.

getEntryDate() - Method in class net.sf.basedb.core.AnnotationType

getEntryDate() - Method in class net.sf.basedb.core.AnnotationTypeCategory

getEntryDate() - Method in class net.sf.basedb.core.ArrayBatch

getEntryDate() - Method in class net.sf.basedb.core.ArrayDesign

getEntryDate() - Method in class net.sf.basedb.core.ArraySlide

getEntryDate() - Method in class net.sf.basedb.core.BioMaterialEvent

Get the date this event was added to the database.

getEntryDate() - Method in class net.sf.basedb.core.BioPlate

getEntryDate() - Method in class net.sf.basedb.core.BioPlateEvent

getEntryDate() - Method in class net.sf.basedb.core.BioSource

getEntryDate() - Method in class net.sf.basedb.core.Client

getEntryDate() - Method in class net.sf.basedb.core.data.AnnotationTypeCategoryData

getEntryDate() - Method in class net.sf.basedb.core.data.AnnotationTypeData

getEntryDate() - Method in class net.sf.basedb.core.data.ArrayBatchData

getEntryDate() - Method in class net.sf.basedb.core.data.ArrayDesignData

getEntryDate() - Method in class net.sf.basedb.core.data.ArraySlideData

getEntryDate() - Method in class net.sf.basedb.core.data.BioMaterialEventData

getEntryDate() - Method in class net.sf.basedb.core.data.BioPlateData

getEntryDate() - Method in class net.sf.basedb.core.data.BioPlateEventData

getEntryDate() - Method in class net.sf.basedb.core.data.BioSourceData

getEntryDate() - Method in class net.sf.basedb.core.data.ClientData

getEntryDate() - Method in class net.sf.basedb.core.data.DerivedBioAssayData

getEntryDate() - Method in class net.sf.basedb.core.data.ExperimentData

getEntryDate() - Method in class net.sf.basedb.core.data.ExtraValueTypeData

getEntryDate() - Method in class net.sf.basedb.core.data.FormulaData

getEntryDate() - Method in class net.sf.basedb.core.data.GroupData

getEntryDate() - Method in class net.sf.basedb.core.data.HardwareData

getEntryDate() - Method in class net.sf.basedb.core.data.ItemSubtypeData

getEntryDate() - Method in class net.sf.basedb.core.data.KitData

getEntryDate() - Method in class net.sf.basedb.core.data.MimeTypeData

getEntryDate() - Method in class net.sf.basedb.core.data.NewsData

getEntryDate() - Method in class net.sf.basedb.core.data.PlateData

getEntryDate() - Method in class net.sf.basedb.core.data.PlateEventData

Get the date this event was added to the database.

getEntryDate() - Method in class net.sf.basedb.core.data.PlateGeometryData

getEntryDate() - Method in class net.sf.basedb.core.data.PlateMappingData

getEntryDate() - Method in class net.sf.basedb.core.data.PlateTypeData

getEntryDate() - Method in class net.sf.basedb.core.data.PluginConfigurationData

getEntryDate() - Method in class net.sf.basedb.core.data.PluginDefinitionData

getEntryDate() - Method in class net.sf.basedb.core.data.PluginTypeData

getEntryDate() - Method in class net.sf.basedb.core.data.ProjectData

getEntryDate() - Method in class net.sf.basedb.core.data.ProtocolData

getEntryDate() - Method in class net.sf.basedb.core.data.QuotaTypeData

getEntryDate() - Method in class net.sf.basedb.core.data.RawBioAssayData

getEntryDate() - Method in interface net.sf.basedb.core.data.RegisteredData

Get the date this item was added to the database.

getEntryDate() - Method in class net.sf.basedb.core.data.ReporterCloneTemplateData

getEntryDate() - Method in class net.sf.basedb.core.data.ReporterData

getEntryDate() - Method in class net.sf.basedb.core.data.ReporterListData

getEntryDate() - Method in class net.sf.basedb.core.data.ReporterTypeData

getEntryDate() - Method in class net.sf.basedb.core.data.RoleData

getEntryDate() - Method in class net.sf.basedb.core.data.SoftwareData

getEntryDate() - Method in class net.sf.basedb.core.data.TagData

getEntryDate() - Method in class net.sf.basedb.core.data.UserData

getEntryDate() - Method in class net.sf.basedb.core.data.UserDeviceData

getEntryDate() - Method in class net.sf.basedb.core.DerivedBioAssay

getEntryDate() - Method in class net.sf.basedb.core.Experiment

getEntryDate() - Method in class net.sf.basedb.core.ExtraValueType

getEntryDate() - Method in class net.sf.basedb.core.Formula

getEntryDate() - Method in class net.sf.basedb.core.Group

getEntryDate() - Method in class net.sf.basedb.core.Hardware

getEntryDate() - Method in class net.sf.basedb.core.ItemSubtype

getEntryDate() - Method in class net.sf.basedb.core.Kit

getEntryDate() - Method in class net.sf.basedb.core.MeasuredBioMaterial

getEntryDate() - Method in class net.sf.basedb.core.MimeType

getEntryDate() - Method in class net.sf.basedb.core.News

getEntryDate() - Method in class net.sf.basedb.core.PhysicalBioAssay

getEntryDate() - Method in class net.sf.basedb.core.Plate

getEntryDate() - Method in class net.sf.basedb.core.PlateEvent

Get the date this event was added to the database.

getEntryDate() - Method in class net.sf.basedb.core.PlateGeometry

getEntryDate() - Method in class net.sf.basedb.core.PlateMapping

getEntryDate() - Method in class net.sf.basedb.core.PlateType

getEntryDate() - Method in class net.sf.basedb.core.PluginConfiguration

getEntryDate() - Method in class net.sf.basedb.core.PluginDefinition

getEntryDate() - Method in class net.sf.basedb.core.PluginType

getEntryDate() - Method in class net.sf.basedb.core.Project

getEntryDate() - Method in class net.sf.basedb.core.Protocol

getEntryDate() - Method in class net.sf.basedb.core.QuotaType

getEntryDate() - Method in class net.sf.basedb.core.RawBioAssay

getEntryDate() - Method in interface net.sf.basedb.core.Registered

Get the date that the item was registered in the database.

getEntryDate() - Method in class net.sf.basedb.core.ReporterCloneTemplate

getEntryDate() - Method in class net.sf.basedb.core.ReporterList

getEntryDate() - Method in class net.sf.basedb.core.ReporterType

getEntryDate() - Method in class net.sf.basedb.core.Role

getEntryDate() - Method in class net.sf.basedb.core.Software

getEntryDate() - Method in class net.sf.basedb.core.Tag

getEntryDate() - Method in class net.sf.basedb.core.User

getEntryDate() - Method in class net.sf.basedb.core.UserDevice

getEnumeration() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

getEnumeration() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction

Get an enumeration of possible values that can be found in the column.

getEnumeration() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

getEnumeration() - Method in class net.sf.basedb.core.ParameterType

Get the list of values to choose from as an enumeration.

getEnumerationValues() - Method in class net.sf.basedb.core.data.AnnotationTypeData

The allowed values if this is an enumeration.

getEnumOptions() - Method in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter

getError() - Method in class net.sf.basedb.core.SimpleProgressReporter

Get error that happened while processing some action that was reported via this progress reporter.

getError() - Method in class net.sf.basedb.util.ContextUtil.ContextResult

Get the exception that caused the error, or null if this is a warning-level object.

getError() - Method in class net.sf.basedb.util.FileCopyRunnable

Get the exception that was thrown when executing the file copy operation.

getErrorclazz() - Method in class net.sf.basedb.clients.web.taglib.table.Cell

getErrorHandler() - Method in class net.sf.basedb.util.extensions.ExtensionContext

getErrorHandler() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext

getErrorHandler() - Method in class net.sf.basedb.util.extensions.InvokationContext

Get the error handler used in this context.

getErrorHandler(String, ErrorHandler) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

getErrorHandler(InvokationContext<? extends A>) - Method in interface net.sf.basedb.util.extensions.ErrorHandlerFactory

Get an error handler for the current context.

getErrorHandler(InvokationContext<? extends Action>) - Method in class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory

getErrorHandler(InvokationContext<? extends Action>) - Method in class net.sf.basedb.util.extensions.RethrowErrorHandlerFactory

getErrorHandlerFactory() - Method in interface net.sf.basedb.util.extensions.ExtensionPoint

Get the error handler factory that should be used with this extension point.

getErrorHandlerFactory() - Method in class net.sf.basedb.util.extensions.ExtensionPointBean

getErrorHandlerFactory() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint

getErrorList() - Method in class net.sf.basedb.core.PluginResponse

Get a list containing detailed error messages if the status is Response.Status.ERROR.

getErrorMessage() - Method in class net.sf.basedb.core.data.FileSetMemberData

The error message if the file validation failed.

getErrorMessage() - Method in class net.sf.basedb.core.FileSetMember

Get the error message if the validation failed.

getErrorOption(String) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

Get the value for an error handling parameter.

getErrors() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper

getEstimatedExecutionTime() - Method in class net.sf.basedb.clients.jobagent.slotmanager.Slot

Get the estimated execution time for this slot.

getEstimatedExecutionTime() - Method in class net.sf.basedb.core.data.JobData

Get the estimated execution time of the job. 0 = <1 minute, 1 = 1 - 10 minutes, 2 = <1 hour, 3 = >1 hour

getEstimatedExecutionTime() - Method in class net.sf.basedb.core.Job

Get the estimated execution time of the job.

getEstimatedExecutionTime() - Method in class net.sf.basedb.core.PluginResponse

Get the estimated execution time of the job.

getEvaluateFormulas() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil

If TRUE, formulas are evaluated and the result is written to the CSV file.

getEvent() - Method in class net.sf.basedb.core.BioMaterialEventSource

Get the event that this information belongs to.

getEvent() - Method in class net.sf.basedb.core.BioPlateEventParticipant

Get the BioPlateEvent.

getEvent() - Method in class net.sf.basedb.core.data.BioMaterialEventSourceData

Get the event that created something from the parent biomaterial.

getEvent() - Method in class net.sf.basedb.core.data.BioPlateEventParticipantData

The bioplate event.

getEvent(PlateEventType) - Method in class net.sf.basedb.core.Plate

Get the event for the specified event type.

getEventDate() - Method in class net.sf.basedb.core.BioMaterialEvent

Get the date this event was done in the lab.

getEventDate() - Method in class net.sf.basedb.core.BioPlate

Get the date this plate was created.

getEventDate() - Method in class net.sf.basedb.core.BioPlateEvent

Get the date this event was done in the lab.

getEventDate() - Method in class net.sf.basedb.core.data.BioMaterialEventData

Get the date this event happened in the lab.

getEventDate() - Method in class net.sf.basedb.core.data.BioPlateData

Get the date this plate was created in the lab.

getEventDate() - Method in class net.sf.basedb.core.data.BioPlateEventData

Get the date this event happened in the lab.

getEventDate() - Method in class net.sf.basedb.core.data.PlateEventData

Get the date this event happened in the lab.

getEventDate() - Method in class net.sf.basedb.core.PlateEvent

Get the date this event was done in the lab.

getEventParticipants() - Method in class net.sf.basedb.core.data.BioPlateData

This is the inverse end.

getEvents() - Method in class net.sf.basedb.core.BioPlate

Get a query returning events that this plate has been a part of.

getEvents() - Method in class net.sf.basedb.core.data.BioPlateEventTypeData

This is the inverse end.

getEvents() - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData

This is the inverse end.

getEvents() - Method in class net.sf.basedb.core.data.PlateData

The event for this plate.

getEvents() - Method in class net.sf.basedb.core.MeasuredBioMaterial

Get a query that returns all events for this biomaterial.

getEvents() - Method in class net.sf.basedb.core.Plate

Get a query that returns all event types for this plate type.

getEventSource(BioMaterial) - Method in class net.sf.basedb.core.BioMaterialEvent

Get information about a biomaterial used as a source to this event.

getEventSources() - Method in class net.sf.basedb.core.BioMaterialEvent

Create a special query that return BioMaterialEventSource objects.

getEventSources(DbControl, int) - Method in class net.sf.basedb.core.BioMaterialEvent

Utility method for finding all sources on a given bioassay position.

getEventType() - Method in class net.sf.basedb.core.BioMaterialEvent

Get the type of event.

getEventType() - Method in class net.sf.basedb.core.BioPlateEvent

Get the event type of this event.

getEventType() - Method in class net.sf.basedb.core.data.BioMaterialEventData

Get the type of event, 1=creation event, 2=hybridization event, 3=other event

getEventType() - Method in class net.sf.basedb.core.data.BioPlateEventData

The type of the event.

getEventTypes() - Method in class net.sf.basedb.core.data.PlateTypeData

The event types defined for this plate type.

getEventTypes() - Method in class net.sf.basedb.core.PlateType

Get a query that returns all event types for this plate type.

getExcelSheet() - Method in class net.sf.basedb.util.parser.FlatFileParser

Get the name of the Excel sheet that should be or is parsed.

getExcelValue(Boolean) - Method in enum class net.sf.basedb.util.formatter.BooleanFormatter.Type

getException() - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress

Get the exception that caused the upload to fail.

getException() - Method in class net.sf.basedb.core.ItemContext

Get the exception that is the cause for the error in ItemContext.configureQuery(DbControl, EntityQuery, boolean).

getExceptionHandler() - Method in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget

getExcludeReportersParameters(DbControl) - Method in class net.sf.basedb.plugins.LowessNormalization

getExecDirectory() - Method in class net.sf.basedb.plugins.Base1PluginExecuter

Get the exec directory as a java.io.File.

getExecLine() - Method in class net.sf.basedb.plugins.Base1PluginExecuter

getExecuteCommand() - Method in class net.sf.basedb.core.data.JobData

The command to send to the plug-in when starting to execute it.

getExecuteCommand() - Method in class net.sf.basedb.core.Job

The command to send to the plug-in when starting to execute it.

getExecutionRequest(ProgressReporter) - Method in class net.sf.basedb.core.PluginResponse

getExecutor() - Method in class net.sf.basedb.plugins.executor.AbstractIOSupport

Get the external program executor that invoked the plug-in.

getExernalPluginParameters(DbControl, BioAssaySet) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

getExistingLinkStatistics(DbControl, ItemQuery<?>, AnyToAnyLinkStatistics.Options) - Static method in class net.sf.basedb.core.AnyToAny

Get information about existing links from the items that are returned by the given query.

getExistingSessionControl(PageContext, boolean) - Static method in class net.sf.basedb.clients.web.Base

Get an existing SessionControl object given a PageContext and optionally check that a user is logged in.

getExistingSessionControl(PageContext, Permission, Item) - Static method in class net.sf.basedb.clients.web.Base

Get an existing SessionControl object given a PageContext and check for generic (role-based) permission to an item type.

getExistingSessionControl(ServletRequest, boolean) - Static method in class net.sf.basedb.clients.web.Base

Get a session control for the BASE web client "net.sf.basedb.clients.web".

getExistingSessionControl(ServletRequest, String, boolean) - Static method in class net.sf.basedb.clients.web.Base

Get an existing SessionControl object given a ServletRequest object and optionally check that a user is logged in.

getExistingSessionControl(ServletRequest, Permission, Item) - Static method in class net.sf.basedb.clients.web.Base

Get an existing SessionControl object given a ServletRequest and check for generic (role-based) permission to an item type.

getExpectedFileSubtype(DbControl, BasicItem) - Method in class net.sf.basedb.util.overview.validator.FileValidator

Get the subtype of the associated file that we expect for the given parent item.

getExpectedHardwareSubtype(DbControl, BasicItem) - Method in class net.sf.basedb.util.overview.validator.HardwareValidator

Get the subtype of the associated hardware that we expect for the given parent item.

getExpectedKitSubtype(DbControl, BasicItem, boolean) - Method in class net.sf.basedb.util.overview.validator.KitValidator

Get the subtype of the associated kit that we expect for the given parent item.

getExpectedProtocolSubtype(DbControl, BasicItem) - Method in class net.sf.basedb.util.overview.validator.ProtocolValidator

Get the subtype of the associated protocol that we expect for the given parent item.

getExpectedSoftwareSubtype(DbControl, BasicItem) - Method in class net.sf.basedb.util.overview.validator.SoftwareValidator

Get the subtype of the associated software that we expect for the given parent item.

getExpectedTagSubtype(DbControl, BasicItem) - Method in class net.sf.basedb.util.overview.validator.TagValidator

Get the subtype of the associated tag that we expect for the given parent item.

getExperiment() - Method in class net.sf.basedb.core.BioAssay

Get the experiment this bioassay belongs to.

getExperiment() - Method in class net.sf.basedb.core.BioAssaySet

Get the experiment this bioassayset belongs to.

getExperiment() - Method in class net.sf.basedb.core.data.BioAssaySetData

Get the experiment this bioassayset belongs to.

getExperiment() - Method in class net.sf.basedb.core.data.JobData

The experiment this job is a part of.

getExperiment() - Method in class net.sf.basedb.core.data.ReporterListData

Get the experiment this reporter list belongs to.

getExperiment() - Method in class net.sf.basedb.core.data.RootRawBioAssayData

Get the experiment this root raw bioassay belongs to.

getExperiment() - Method in class net.sf.basedb.core.data.TransformationData

Get the experiment this bioassayset belongs to.

getExperiment() - Method in class net.sf.basedb.core.data.VirtualDbData

Get the experiment that stores it's data in this virtual database.

getExperiment() - Method in class net.sf.basedb.core.DataCube

Get the experiment this data cube belongs to.

getExperiment() - Method in class net.sf.basedb.core.ExtraValue

Get the experiment this extra value belongs to.

getExperiment() - Method in class net.sf.basedb.core.Job

Get the experiment this job is a part of.

getExperiment() - Method in class net.sf.basedb.core.ReporterCloneBatcher

Get the current experiment this batcher is used with.

getExperiment() - Method in class net.sf.basedb.core.ReporterList

Get the experiment this reporter list belongs to.

getExperiment() - Method in class net.sf.basedb.core.RootRawBioAssay

Get the experiment this root raw bioassay belongs to.

getExperiment() - Method in class net.sf.basedb.core.Transformation

Get the experiment this transformation belongs to.

getExperiment() - Method in class net.sf.basedb.core.VirtualDb

Get the experiment this set of tables stores data for.

getExperiment(DbControl) - Method in class net.sf.basedb.clients.web.ExperimentExplorer

Get the experiment that is currently beeing explored.

getExperimentalFactorField(String, String) - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter

Get an experimental factor assay field.

getExperimentalFactors() - Method in class net.sf.basedb.core.data.ExperimentData

The annotation types which describes the experimental factors for this experiment.

getExperimentalFactors() - Method in class net.sf.basedb.core.Experiment

Get a query that returns all annotation types used as experimental factors for this experiment.

getExperimentDesign() - Method in class net.sf.basedb.core.data.ExperimentData

Get the experimental design for this experiment.

getExperimentDesign() - Method in class net.sf.basedb.core.Experiment

Get the a text describing the experimental design.

getExperiments() - Method in class net.sf.basedb.core.data.AnnotationTypeData

This is the inverse end.

getExperiments() - Method in class net.sf.basedb.core.data.RawBioAssayData

This is the inverse end.

getExperiments() - Method in class net.sf.basedb.core.RawBioAssay

Get a query that returns all experiments where this raw bioassay is used.

getExperimentType() - Method in class net.sf.basedb.core.data.ExperimentData

Get the experimental type for this experiment.

getExperimentType() - Method in class net.sf.basedb.core.Experiment

Get the a text describing the experiment type.

getExpirationDate() - Method in class net.sf.basedb.core.data.KitData

Get expiration date for the kit.

getExpirationDate() - Method in class net.sf.basedb.core.data.UserData

Get the expiration date for this user account, or null if no expiration date is set.

getExpirationDate() - Method in class net.sf.basedb.core.Kit

Get the expiration date of the kit.

getExpirationDate() - Method in class net.sf.basedb.core.User

Get the expire date of the account.

getExplorer(BioAssaySet) - Static method in class net.sf.basedb.clients.web.ExperimentExplorer

Get the existing experiment explorer for a bioassayset or create a new one if none exist yet.

getExportable() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn

getExportableFields(DbControl, BioAssaySet) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin

getExportableFields(DbControl, BioAssaySet) - Method in class net.sf.basedb.plugins.BfsExporterPlugin

getExporter(DbControl, boolean, boolean) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

Get an instance of the exporter plug-in.

getExportFormatter() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

getExportFormatter() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction

Get a formatter that converts the exported value to a string that is written to the file.

getExportproperty() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

getExportProperty() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

getExportProperty() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction

Override the default property when this column is used for exporting.

getExporttitle() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

getExportTitle() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

getExportTitle() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction

Alternative column title that should be used when exporting data from a table.

getExportValue(RelatedItemHelper, Annotatable, SourceItemTransformer) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn

Alternate implementation for loading data.

getExportValue(RelatedItemHelper, Annotatable, SourceItemTransformer) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemExtensionColumn

getExportValue(RelatedItemHelper, Annotatable, SourceItemTransformer) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemMultiHopColumn

getExportValue(DbControl, I) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

This implementation simply forward to ListColumnAction.getValue(DbControl, Object).

getExportValue(DbControl, I) - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction

Get the value that should be used when exporting to a file.

getExportValue(DbControl, I) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory.PropertyPathAction

getExportValue(DbControl, Annotatable) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn

We finalize this implementation to make sure that the helper implementation always get a chance to re-cycle transactions.

getExpression() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

Get the full expression that defines the targeted item and property.

getExpression() - Method in class net.sf.basedb.core.query.ExpressionSelect

getExpression() - Method in interface net.sf.basedb.core.query.Select

Get the expression object representing the selected expression.

getExpression() - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField

Get the configured express.

getExpression(DbControl, DynamicQuery, BioAssaySet, boolean) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField

getExpression(DbControl, DynamicQuery, BioAssaySet, boolean) - Method in interface net.sf.basedb.util.export.spotdata.DynamicField

Get an expression that selects the data that should be exported.

getExpression(DbControl, DynamicQuery, BioAssaySet, boolean) - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField

Converts the configured JEP expression using the BioAssaySetUtil.createJepExpression(DbControl, String, DynamicQuery) method.

getExpression(DbControl, DynamicQuery, BioAssaySet, boolean) - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField

Returns the configured expression.

getExpressions() - Method in class net.sf.basedb.core.IntensityFormula

Get the expressions used to calculate the intensities.

getExtended(String) - Method in class net.sf.basedb.core.authentication.ExtraUserInformation

Get an extended property value.

getExtended(String) - Method in interface net.sf.basedb.core.data.ExtendableData

Get the value of an extended property.

getExtended(String) - Method in class net.sf.basedb.core.data.RawData

getExtended(String) - Method in class net.sf.basedb.core.data.ReporterData

getExtended(String) - Method in class net.sf.basedb.core.data.UserData

getExtended(String) - Method in class net.sf.basedb.core.User

Gets an extended property with a certain name

getExtendedPropertyFiles() - Static method in class net.sf.basedb.core.Application

Get the path to the XML file containing extended properties.

getExtendedPropertyFormatter(SessionControl, ExtendedProperty) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory

Get a formatter for an extended property.

getExtends() - Method in interface net.sf.basedb.util.extensions.Extension

Get the ID of the extension point this extension is extending.

getExtends() - Method in class net.sf.basedb.util.extensions.ExtensionBean

getExtends() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension

getExtension() - Method in class net.sf.basedb.clients.web.fileupload.UploadedFile

Get the extension of the original filename.

getExtension() - Method in class net.sf.basedb.core.data.DataFileTypeData

Get the extension that files of this type usually have.

getExtension() - Method in class net.sf.basedb.core.data.MimeTypeData

Get the extension for this MimeType item.

getExtension() - Method in class net.sf.basedb.core.DataFileType

Get the common file extension for data files of this type.

getExtension() - Method in class net.sf.basedb.core.MimeType

Get the extension for this MimeType item.

getExtension() - Method in class net.sf.basedb.util.extensions.ActionIterator

Get the extension that created the current action.

getExtension() - Method in class net.sf.basedb.util.extensions.ExtensionContext

getExtension() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext

Always null, since this is an extension point context.

getExtension() - Method in class net.sf.basedb.util.extensions.InvokationContext

Get information about the extension.

getExtension(String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Get the extension with a given ID.

getExtension(String) - Method in class net.sf.basedb.util.extensions.Registry

Get the extension with a given ID.

getExtensionClassLoader() - Method in class net.sf.basedb.clients.web.extensions.XJspCompiler

Get a class loader that can load classes from the current web application as well as the extensions JAR file.

getExtensionColumns() - Method in class net.sf.basedb.clients.web.taglib.table.Table

getExtensionId() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

Get the extension id from the expression.

getExtensionId() - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog

Get the extension id of the log.

getExtensionPoint() - Method in class net.sf.basedb.util.extensions.ActionIterator

Get the extension point that the current action belongs to.

getExtensionPoint() - Method in class net.sf.basedb.util.extensions.ExtensionContext

getExtensionPoint() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext

getExtensionPoint() - Method in class net.sf.basedb.util.extensions.InvokationContext

Get information about the extension point.

getExtensionPoint() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension

Get the extension point this extension is registered with.

getExtensionPoint(String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Get the extension point with a given ID.

getExtensionPoint(String) - Method in class net.sf.basedb.util.extensions.Registry

Get the extension point with a given ID.

getExtensionPoints() - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Get an list returning all registered extension points.

getExtensionPoints() - Method in class net.sf.basedb.util.extensions.Registry

Get a list with all registered extension points.

getExtensionPoints() - Method in class net.sf.basedb.util.extensions.xml.XmlLoader

Get a list with all loaded extension points.

getExtensions() - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Get a list returning all registered extensions.

getExtensions() - Method in class net.sf.basedb.plugins.Bzip2FileUnpacker

Return a set containing the strings [ bz2 ].

getExtensions() - Method in class net.sf.basedb.plugins.GzipFileUnpacker

Return a set containing the strings [ gz ].

getExtensions() - Method in class net.sf.basedb.plugins.TarFileUnpacker

Return a set containing the strings [ tar, tar.gz, tgz, tar.bz2 ].

getExtensions() - Method in class net.sf.basedb.plugins.ZipFileUnpacker

Return a set containing the strings [ zip, jar ].

getExtensions() - Method in class net.sf.basedb.util.extensions.Registry

Get a list with all registered extensions.

getExtensions() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint

Get all extensions registered with this extension point.

getExtensions() - Method in class net.sf.basedb.util.extensions.xml.XmlLoader

Get a list with all loaded extensions.

getExtensions() - Method in interface net.sf.basedb.util.zip.FileUnpacker

Get the file extensions that this unpacker supports.

getExtensions(String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Get a list returning all registered extensions for a specific extension point.

getExtensions(String) - Method in class net.sf.basedb.util.extensions.Registry

Get a list with all registered extensions for a given extension point.

getExtensionsFile() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile

Get the underlying extensions file (for readin information)

getExtensionsFile() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults.FileResults

getExtensionsManager() - Static method in class net.sf.basedb.core.Application

getExternalClientId() - Method in class net.sf.basedb.core.SessionControl

Get the external id of the Client application that created this SessionControl.

getExternalId() - Method in class net.sf.basedb.core.AnnotationType

Get the external id of the annotation type.

getExternalId() - Method in class net.sf.basedb.core.authentication.AuthenticatedUser

Get the external id for the user.

getExternalId() - Method in class net.sf.basedb.core.BioMaterial

Get the external id of the biomaterial.

getExternalId() - Method in class net.sf.basedb.core.BioPlate

Gets the external id of this bio plate

getExternalId() - Method in class net.sf.basedb.core.Client

Get the external id for this Client item.

getExternalId() - Method in class net.sf.basedb.core.data.AnnotationTypeData

Get the external id for the biomaterial

getExternalId() - Method in class net.sf.basedb.core.data.BioMaterialData

Get the external id for the biomaterial

getExternalId() - Method in class net.sf.basedb.core.data.BioPlateData

Get the external id for the biomaterial

getExternalId() - Method in class net.sf.basedb.core.data.ClientData

Get the external id for this Client item.

getExternalId() - Method in class net.sf.basedb.core.data.DataFileTypeData

Get the external id for the item.

getExternalId() - Method in class net.sf.basedb.core.data.ExtraValueTypeData

Get the external id for this ExtraValueType item.

getExternalId() - Method in class net.sf.basedb.core.data.FeatureData

Get the external id for this FeatureData item.

getExternalId() - Method in class net.sf.basedb.core.data.HelpData

Get the external id for this Help item.

getExternalId() - Method in class net.sf.basedb.core.data.ItemListData

Get the external id for this ItemList item.

getExternalId() - Method in class net.sf.basedb.core.data.JobAgentData

Get the external ID for the job agent.

getExternalId() - Method in class net.sf.basedb.core.data.JobData

External ID of a job running on an external system.

getExternalId() - Method in class net.sf.basedb.core.data.PlatformData

Get the external id for the item.

getExternalId() - Method in class net.sf.basedb.core.data.PlatformVariantData

Get the external id for the item.

getExternalId() - Method in class net.sf.basedb.core.data.ProtocolData

Get the external id for the protocol.

getExternalId() - Method in class net.sf.basedb.core.data.ReporterData

Get the external id for this ReporterData item.

getExternalId() - Method in class net.sf.basedb.core.data.ReporterListData

Get the external id for this ReporterList item.

getExternalId() - Method in class net.sf.basedb.core.data.UserData

Get the external ID for the user account.

getExternalId() - Method in class net.sf.basedb.core.DataFileType

Get the external id for the data file type.

getExternalId() - Method in class net.sf.basedb.core.ExtraValueType

Get the external id for this ExtraValueType item.

getExternalId() - Method in class net.sf.basedb.core.Help

Get the external id for this Help item.

getExternalId() - Method in class net.sf.basedb.core.ItemList

Get the external id for this list.

getExternalId() - Method in class net.sf.basedb.core.Job

Get the external ID of a job running on an external server.

getExternalId() - Method in class net.sf.basedb.core.JobAgent

Get the external id for the job agent.

getExternalId() - Method in class net.sf.basedb.core.Platform

Get the external id for the platform.

getExternalId() - Method in class net.sf.basedb.core.PlatformVariant

Get the external id for the platform variant.

getExternalId() - Method in class net.sf.basedb.core.Protocol

Get the external id of the protocol.

getExternalId() - Method in class net.sf.basedb.core.RawDataBatcher.ReporterProxy

getExternalId() - Method in class net.sf.basedb.core.ReporterList

Get the external id for this ReporterList item.

getExternalId() - Method in class net.sf.basedb.core.User

Get the external id for the user account.

getExtract() - Method in class net.sf.basedb.core.data.DerivedBioAssayData

Get the extract that this bioassay is related to.

getExtract() - Method in class net.sf.basedb.core.DerivedBioAssay

Get the extract that is the parent of the data in this derived bioassay.

getExtract(Annotatable) - Static method in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper

Get the extract to use.

getExtract(DerivedBioAssay) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader

Get the extract that is associated with the current derived bioassay

getExtract(RawBioAssay) - Method in class net.sf.basedb.util.overview.loader.RawBioAssayLoader

Get the extract that is associated with the current raw bioassay

getExtractChain(DbControl, Node) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader

getExtractChain(DbControl, Node) - Method in class net.sf.basedb.util.overview.loader.RawBioAssayLoader

getExtractChain(Node) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader

getExtracts() - Method in class net.sf.basedb.core.Sample

Get a query that returns all extracts created from this sample.

getExtracts(int) - Method in class net.sf.basedb.core.PhysicalBioAssay

Get a query that returns extracts connected to this bioassay.

getExtraField() - Method in interface net.sf.basedb.clients.web.extensions.login.LoginFormAction

An optional extra field on the login form.

getExtraField() - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean

getExtraFilesDirectory(DbControl, String) - Method in class net.sf.basedb.plugins.executor.BaseFileImporterSupport

getExtraFilesDirectory(DbControl, String) - Method in class net.sf.basedb.plugins.executor.BfsImporterSupport

getExtraFilesDirectory(DbControl, String) - Method in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport

getExtraFloat(String) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo

Get the extra value type that has the given external id.

getExtraFloatParsers() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo

Get the list of extra value parsers that exists for this section.

getExtraInformation() - Method in class net.sf.basedb.core.authentication.AuthenticatedUser

Get extra information about the user.

getExtraNo() - Method in class net.sf.basedb.core.data.DataCubeExtraValueData

The number of this extra value in the data cube.

getExtraNo() - Method in class net.sf.basedb.core.DataCubeExtraValue

Get the extra value number.

getExtraNo() - Method in class net.sf.basedb.core.ExtraValue

Get the number in the data cube of the extra values.

getExtraValue() - Method in class net.sf.basedb.core.ExtraValueExpression

getExtraValue() - Method in class net.sf.basedb.core.SpotExtraValueBatcher

Get the extra value item representing all extra values.

getExtraValue(ExtraValueType) - Method in class net.sf.basedb.core.BioAssaySet

Get the extra value of the specified type in this bioassayset.

getExtraValueField(String, ExtraValue.CoordinateType, String) - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter

Get an extra value dynamic field.

getExtraValueFields(DbControl, BioAssaySet) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin

getExtraValueFields(DbControl, BioAssaySet) - Method in class net.sf.basedb.plugins.BfsExporterPlugin

getExtraValueJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicPositionQueryJoiners

Get a joiner instance for extra values for the specified join type.

getExtraValueJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicSpotQueryJoiners

Get a joiner instance for extra values for the specified join type.

getExtraValues() - Method in class net.sf.basedb.core.BioAssaySet

Get a query returning the extra values that are part of this bioassayset.

getExtraValues() - Method in class net.sf.basedb.core.data.BioAssaySetData

The extra values calculated for this bioassayset.

getExtraValues() - Method in class net.sf.basedb.core.data.DataCubeData

This is the inverse end.

getExtraValues() - Method in class net.sf.basedb.core.data.ExtraValueTypeData

This is the inverse end.

getExtraValueType() - Method in class net.sf.basedb.core.data.ExtraValueData

Get the type of this extra value.

getExtraValueType() - Method in class net.sf.basedb.core.ExtraValue

Get the type of the extra values.

getExtraValueTypes() - Method in class net.sf.basedb.core.BioAssaySet

Get a query returning all extra values types that are used in this bioassay set.

getFactories() - Static method in class net.sf.basedb.util.uri.ConnectionManagerUtil

Get a list with all connection manager factories.

getFactory(String) - Static method in class net.sf.basedb.util.uri.ConnectionManagerUtil

Get the connection manager factory with the given extension id.

getFactoryParameters(Object) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader

Get a XML-like string representation of the parameters that was used to initialise a factory.

getFailures() - Method in class net.sf.basedb.util.overview.GenericOverview

Get a list containing all validation failures.

getFailureSummary() - Method in interface net.sf.basedb.util.overview.extensions.ValidationRuleAction

Get a short summary that is displayed when the validation fails

getFailureSummary() - Method in class net.sf.basedb.util.overview.Validator

Get a short summary that is displayed when the validation fails

getFallbackLocale(String, Locale) - Method in class net.sf.basedb.util.resources.Utf8PropertiesResourceBundleControl

We don't need a fallback locale.

getFastLoader(DbControl) - Method in class net.sf.basedb.core.AnnotationType

Create a loader that can be used for fast loading of annotation values for multiple items.

getFastLoader(DbControl, Item, String, Item) - Static method in class net.sf.basedb.core.AnyToAny

Create an optimized implementation for loading the target item of a given named link from multiple source items.

getFavicon() - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory

getFavicon() - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory.MySkinAction

getFavicon() - Method in interface net.sf.basedb.clients.web.extensions.skin.SkinAction

Get the full path to a favicon for the BASE site.

getFavicon() - Method in class net.sf.basedb.clients.web.taglib.Page

getFax() - Method in class net.sf.basedb.core.authentication.ExtraUserInformation

The fax number to the user.

getFax() - Method in class net.sf.basedb.core.data.UserData

Get the fax number to the user, or null if unknown.

getFax() - Method in class net.sf.basedb.core.User

Get the fax number to the user, or null if unknown.

getFeature() - Method in class net.sf.basedb.core.data.RawData

The feature this raw data is connected with.

getFeature(RawDataBatcher.FeatureProxy) - Method in class net.sf.basedb.core.RawDataBatcher.FeatureInfo

getFeatureBatcher(FeatureIdentificationMethod, Job) - Method in class net.sf.basedb.core.ArrayDesign

Get a feature batcher which can be used to add regular features to the array design.

getFeatureById(int) - Method in class net.sf.basedb.core.ArrayDesign

Get a feature when you know the id.

getFeatureById(int, boolean) - Method in class net.sf.basedb.core.ArrayDesign

Get a feature when you know the id.

getFeatureCoordinate(FeatureData) - Static method in class net.sf.basedb.core.Feature

Get the coordinate of the feature.

getFeatureDiameter() - Method in class net.sf.basedb.core.ArrayDesignBlock

Get the expected diameter of spots on the slide.

getFeatureDiameter() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData

The expected diameter of spots.

getFeatureIdentificationMethod() - Method in class net.sf.basedb.core.ArrayDesign

Get the method used to identify features on this array design.

getFeatureIdentificationMethod() - Method in class net.sf.basedb.core.data.ArrayDesignData

The method to use for identiying features. 1 = COORDINATES, 2 = POSITION, 3 = FEATURE_ID

getFeatures() - Method in class net.sf.basedb.core.ArrayDesign

Get a query that returns the regular features of this array design.

getFeatures() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData

Used by Hibernate to link with features.

getFetchSize() - Method in class net.sf.basedb.core.hibernate.QueryWrapper

getField() - Method in class net.sf.basedb.plugins.BfsExporterPlugin.ExtendedExportableField

getFile() - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext

Get the current file.

getFile() - Method in interface net.sf.basedb.core.data.FileAttachableData

Get the file that is attached to the item.

getFile() - Method in class net.sf.basedb.core.data.FileSetMemberData

Get the file.

getFile() - Method in class net.sf.basedb.core.data.ProtocolData

getFile() - Method in interface net.sf.basedb.core.FileAttachable

Get the file that is attached to the item.

getFile() - Method in class net.sf.basedb.core.FileSetMember

Get the file this item is representing in the file set.

getFile() - Method in class net.sf.basedb.core.plugin.ExportOutputStream

If the export stream is going to a BASE File object, use this method to access it.

getFile() - Method in class net.sf.basedb.core.Protocol

getFile() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile

Get the underlying file on the file system.

getFile() - Method in class net.sf.basedb.util.FileExportOutputStream

getFile(int) - Method in class net.sf.basedb.util.bfs.MetadataModel

Get the file entry with a given index.

getFile(String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Get information about an installed extensions file.

getFile(String) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload

Get the file information for an uplodaded file.

getFile(String) - Method in class net.sf.basedb.util.bfs.BaseInputStreamLocator

getFile(String) - Method in class net.sf.basedb.util.bfs.MetadataModel

Get the file entry for a given key.

getFile(DbControl, Directory, String, boolean) - Static method in class net.sf.basedb.core.File

Get a File item when you know the directory and filename.

getFileByObjectKey(ObjectKey<?>) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Find out which file the given object is defined in.

getFileByObjectKey(ObjectKey<?>) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager

Find out which file the object with the given key was defined.

getFileByURI(String) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager

Get the extension file that is located at the given URI.

getFileContext() - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerUtil

Get the file context.

getFileCount() - Method in class net.sf.basedb.util.bfs.MetadataModel

Get the number of entries in the 'files' section.

getFileExtension() - Method in class net.sf.basedb.util.zip.Bzip2FilePacker

getFileExtension() - Method in interface net.sf.basedb.util.zip.FilePacker

Gets the extension that files, packed with this tool, should have, for example, zip or tar.gz Don't include the first dot!

getFileExtension() - Method in class net.sf.basedb.util.zip.GzipFilePacker

getFileExtension() - Method in class net.sf.basedb.util.zip.TarFilePacker

getFileExtension() - Method in class net.sf.basedb.util.zip.ZipFilePacker

getFileFormatParameter() - Static method in class net.sf.basedb.plugins.BaseFileExporterPlugin

Create a plug-in parameter that asks for the BASEFile subtype to use in the export.

getFileFormatParameter() - Static method in class net.sf.basedb.plugins.BfsExporterPlugin

Create a plug-in parameter that asks for the BFS subtype to use in the export.

getFileId() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay

Get the id of the child bioassay as it appears in the BASEfile.

getFileIterator() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

Get an iterator that returns the files to be imported.

getFileIterator() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter

getFileLinks(String, File, String) - Static method in class net.sf.basedb.clients.web.Base

Get view/download links for a file.

getFilename() - Method in class net.sf.basedb.clients.web.fileupload.UploadedFile

Get the original filename of the uploaded file.

getFilename() - Method in class net.sf.basedb.core.Path

Get the filename part of the path.

getFilename() - Method in class net.sf.basedb.core.plugin.ImportInputStream

Get the name of the source.

getFilename() - Method in class net.sf.basedb.util.bfs.AnnotationParser

Get the file name that this parser is reading from.

getFilename() - Method in class net.sf.basedb.util.bfs.AnnotationWriter

Get the file name that this writer is printing to.

getFilename() - Method in interface net.sf.basedb.util.bfs.BfsParser

Get the filename of the file that is being parsed.

getFilename() - Method in class net.sf.basedb.util.bfs.DataParser

Get the file name that this parser is reading from.

getFilename() - Method in class net.sf.basedb.util.bfs.DataWriter

Get the file name that this writer is printing to.

getFilename() - Method in class net.sf.basedb.util.bfs.MetadataParser

Get the file name that this writer is printing to.

getFilename() - Method in class net.sf.basedb.util.bfs.MetadataWriter

Get the file name that this writer is printing to.

getFilename() - Method in class net.sf.basedb.util.FileImportInputStream

Calls CommonItem.getName().

getFilename() - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser

getFileNameGeneratorParameter() - Static method in class net.sf.basedb.plugins.BfsExporterPlugin

Create a plug-in parameter that asks for the file name generation strategy.

getFileOnlyRawDataTypes() - Static method in class net.sf.basedb.core.RawDataTypes

Get the raw data types that are representations of file-only Platform:s.

getFiles() - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Get an list returning all XML/JAR files which contains installed extensions.

getFiles() - Method in class net.sf.basedb.core.data.DirectoryData

This is the inverse end.

getFiles() - Method in class net.sf.basedb.core.data.FileServerData

This is the inverse end.

getFiles() - Method in class net.sf.basedb.core.Directory

Get a query that return all files in this directory.

getFiles() - Method in class net.sf.basedb.core.FileServer

Get a query returning all files that has been registered with this server.

getFiles() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager

Get a list of all extension files managed by this manager.

getFileServer() - Method in class net.sf.basedb.core.data.FileData

Get the associated FileServerData item.

getFileServer() - Method in class net.sf.basedb.core.File

Get the file server on which the external file is located.

getFileSet() - Method in class net.sf.basedb.core.ArrayDesign

getFileSet() - Method in class net.sf.basedb.core.BioAssaySet

getFileSet() - Method in class net.sf.basedb.core.data.ArrayDesignData

getFileSet() - Method in class net.sf.basedb.core.data.BioAssaySetData

getFileSet() - Method in class net.sf.basedb.core.data.DerivedBioAssayData

getFileSet() - Method in class net.sf.basedb.core.data.ExtraValueData

getFileSet() - Method in class net.sf.basedb.core.data.FileSetMemberData

Get the file set this file belongs to.

getFileSet() - Method in interface net.sf.basedb.core.data.FileStoreEnabledData

Get the file set attached to this item.

getFileSet() - Method in class net.sf.basedb.core.data.RawBioAssayData

getFileSet() - Method in class net.sf.basedb.core.DerivedBioAssay

getFileSet() - Method in class net.sf.basedb.core.ExtraValue

getFileSet() - Method in class net.sf.basedb.core.FileSetMember

Get the file set the file is a member of.

getFileSet() - Method in interface net.sf.basedb.core.FileStoreEnabled

Get the file set that collects all files that holds data for this item.

getFileSet() - Method in class net.sf.basedb.core.RawBioAssay

getFileSetMember() - Method in class net.sf.basedb.util.overview.Fix

getFileSetMembers() - Method in class net.sf.basedb.core.data.DataFileTypeData

This is the inverse end.

getFileSize() - Method in class net.sf.basedb.util.bfs.AnnotationParser

Get the size in bytes of the file that this parser is reading from.

getFileSize() - Method in interface net.sf.basedb.util.bfs.BfsParser

Get the size of the file that is being parsed.

getFileSize() - Method in class net.sf.basedb.util.bfs.DataParser

Get the size in bytes of the file that this parser is reading from.

getFileSize() - Method in class net.sf.basedb.util.bfs.MetadataParser

Get the size in bytes of the file that this parser is reading from.

getFileSize() - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser

getFileStoreEnabledItems() - Static method in class net.sf.basedb.core.Metadata

Get a set containing all FileStoreEnabled item types.

getFileType() - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext

Get the current data file type.

getFileType() - Method in class net.sf.basedb.core.data.MimeTypeData

Get the associated ItemSubtypeData item.

getFileType() - Method in class net.sf.basedb.core.MimeType

Get the associated file subtype item.

getFileType(DataFileType, PlatformVariant, boolean) - Method in class net.sf.basedb.core.Platform

Get information about a file type that has been registered with this platform/variant.

getFileTypes() - Method in class net.sf.basedb.core.data.ItemSubtypeData

The file types that can be used on items of this subtype.

getFileTypes() - Method in class net.sf.basedb.core.data.PlatformData

The file types that can be used on this platform.

getFileTypes() - Method in class net.sf.basedb.core.data.PlatformVariantData

The additional file types that can be used on this platform variant.

getFileTypes(boolean) - Method in class net.sf.basedb.core.PlatformVariant

Get a query returning file types registered with this platform variant.

getFileTypes(PlatformVariant, boolean) - Method in class net.sf.basedb.core.Platform

Get the file types registered with this platform.

getFileValues(String) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload

Get the file information for uplodaded files.

getFilltext() - Method in class net.sf.basedb.clients.web.taglib.menu.Menu

getFilterable() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn

getFilterAnnotationType(DbControl) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

getFilterBatcher() - Method in class net.sf.basedb.core.BioAssaySet

Get a batcher used to insert the position/column coordinates that remain after some filter has been applied to the spot data of a bioassayset.

getFilterclass() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

getFilterClass() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

getFilterClass() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction

Extra CSS class to add to the filter table cell.

getFilterGroup() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData

Get the group for this filter.

getFilterGroup() - Method in class net.sf.basedb.core.SyncFilter

Get the group this synchronization filter belongs to.

getFilterItemList(DbControl) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

getFilterNo() - Method in class net.sf.basedb.core.data.DataCubeFilterData

The number of this filter in the data cube.

getFilterNo() - Method in class net.sf.basedb.core.DataCubeFilter

Get the number of this filter.

getFilterproperty() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

getFilterProperty() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

getFilterProperty() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction

Override the default property when this column is used for filtering.

getFilterRestriction(String, int, DbControl, EntityQuery) - Method in class net.sf.basedb.core.ItemContext

Create a restriction from a property filter on the given filter row.

getFilterRestriction(String, DbControl, EntityQuery) - Method in class net.sf.basedb.core.ItemContext

Create a restriction from a property filter on filter row 0.

getFilterrows() - Method in class net.sf.basedb.clients.web.taglib.table.Table

getFilterRows() - Method in class net.sf.basedb.core.ItemContext

Get the number of filter rows to display on the list page.

getFilterRows() - Method in class net.sf.basedb.core.SyncFilter

Get the number of filter rows in this filter.

getFilters() - Method in class net.sf.basedb.core.data.DataCubeData

This is the inverse end.

getFiltertext() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

getFilterText() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

getFilterText() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction

A text to display in the filter cell when the column is not filterable.

getFingerprintType() - Method in class net.sf.basedb.core.data.FileServerData

Get the type of SSH fingerprint.

getFingerprintType() - Method in class net.sf.basedb.core.FileServer

Get the type of the SSH fingerprint.

getFirst(ExtensionsInvoker<ConnectionManagerFactory>) - Static method in class net.sf.basedb.util.uri.ConnectionManagerUtil

Get the first factory returned by the invoker.

getFirstAssayFieldIndex() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo

The index of the first data column that contains assay data.

getFirstColumn() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo

Get the column number for the first column that contains data.

getFirstMatching(DbControl, ItemQuery<T>, String, PropertyFilter) - Static method in class net.sf.basedb.clients.web.Base

getFirstNode(Filter<? super Node>) - Method in class net.sf.basedb.util.overview.Node

Find the first node (including this) that matches a filter.

getFirstNull(Object[]) - Static method in class net.sf.basedb.core.query.Expressions

Test if there is null in the array.

getFirstNull(Object[]) - Static method in class net.sf.basedb.core.query.Restrictions

Test if there is null in the array.

getFirstParent(Filter<? super Node>) - Method in class net.sf.basedb.util.overview.Node

Find the first parent node that matches a filter.

getFirstResult() - Method in class net.sf.basedb.core.AbstractQuery

getFirstResult() - Method in class net.sf.basedb.core.hibernate.QueryWrapper

getFirstResult() - Method in interface net.sf.basedb.core.query.Query

The number of the row the query should start returning.

getFirstRow() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo

Get the row number for the first row that contains data.

getFixes() - Method in class net.sf.basedb.util.overview.Failure

Get a list of suggested fixes.

getFkColumns() - Method in class net.sf.basedb.core.dbengine.TableInfo.ForeignKeyInfo

getFloat(int) - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult

getFloat(int) - Method in class net.sf.basedb.core.DynamicResultIterator.SqlResultImpl

getFloat(int) - Method in interface net.sf.basedb.core.query.SqlResult

Get the value of the specified column as a float.

getFloat(int) - Method in class net.sf.basedb.util.parser.FlatFileParser.Data

Shortcut for getFloat(index, null, true)

getFloat(int, NumberFormat, boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser.Data

Get the value as a float.

getFloat(int, NumberFormat, boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser.ExcelData

getFloat(String) - Static method in class net.sf.basedb.util.Values

Convert a string to an float.

getFloat(String[]) - Static method in class net.sf.basedb.util.Values

Convert an array of strings to an array of Float:s.

getFloat(String, float) - Static method in class net.sf.basedb.util.Values

Convert a string to an integer.

getFloat(String, Float) - Static method in class net.sf.basedb.util.Values

getFloat(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.ColumnMapper

getFloat(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.CompoundMapper

getFloat(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.ConstantMapper

getFloat(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.CropStringMapper

getFloat(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.JepMapper

getFloat(FlatFileParser.Data) - Method in interface net.sf.basedb.util.parser.Mapper

Get the value for the line of data as a float.

getFloat(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.NullIfExceptionMapper

getFloatOption(String, Float) - Method in class net.sf.basedb.core.AnnotationType

Get an option and convert the value to a float.

getFloatValues() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink

getFlushMode() - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

getFlushMode() - Method in class net.sf.basedb.core.hibernate.SessionWrapper

getForeignKeys() - Method in class net.sf.basedb.core.dbengine.TableInfo

Get information about the foreign keys in the table.

getForInsert(Object, Map, SharedSessionContractImplementor) - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter

Get the value of the extended property.

getFormat() - Method in class net.sf.basedb.util.excel.ExcelValue

Get the format string.

getFormatName() - Method in class net.sf.basedb.plugins.Bzip2FileUnpacker

getFormatName() - Method in class net.sf.basedb.plugins.GzipFileUnpacker

getFormatName() - Method in class net.sf.basedb.plugins.TarFileUnpacker

getFormatName() - Method in class net.sf.basedb.plugins.ZipFileUnpacker

getFormatName() - Method in interface net.sf.basedb.util.zip.FileUnpacker

Get the name of the compressed file format this unpacker supports.

getFormatParameter() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport

getFormats(String) - Method in class net.sf.basedb.util.resources.Utf8PropertiesResourceBundleControl

This control only handle property files.

getFormattedAndSortedFilters(Collection<PropertyFilter>, Formatter<PropertyFilter>) - Static method in class net.sf.basedb.core.SyncFilter

Utility method for formatting and sorting a list of property filters.

getFormatter() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

getFormatter() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction

Get a formatter that converts the current value to a string that is displayed in the column.

getFormatter() - Method in class net.sf.basedb.clients.web.taglib.table.Cell

getFormatter() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

getFormatter() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn

getFormatter() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField

getFormatter() - Method in class net.sf.basedb.util.export.spotdata.AnnotationAssayField

getFormatter() - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField

getFormatter() - Method in interface net.sf.basedb.util.export.spotdata.ExportableField

Get a formatter that converts the values in this field to strings.

getFormatter() - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField

getFormatter() - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField

getFormatter(Object) - Method in class net.sf.basedb.util.formatter.MultiFormatter

getFormatter(String) - Method in class net.sf.basedb.clients.web.taglib.table.Table

getFormatter(InvokationContext, String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

Create a formatter instance that should be used for the online table.

getFormatter(Formatter<T>) - Method in class net.sf.basedb.core.Unit

Create a formatter for formatting values with this unit.

getFormName() - Method in class net.sf.basedb.clients.web.fileupload.UploadedFile

Get the name of the form field that this file was selected in.

getFormula(int) - Method in class net.sf.basedb.core.Formula

Get an expression.

getFormulaField(String, String) - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter

Get a formula dynamic field.

getFormulaFields(DbControl, BioAssaySet) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin

getFormulaFields(DbControl, BioAssaySet) - Method in class net.sf.basedb.plugins.BfsExporterPlugin

getFormulaFormatter(SessionControl, Formula) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory

Get a formatter that knows how to format results from formulas.

getFormulas() - Method in class net.sf.basedb.core.data.FormulaData

Get the list of formulas.

getFormulas() - Method in class net.sf.basedb.core.Formula

Get all expressions as an unmodifiable list.

getFormulaType() - Method in class net.sf.basedb.core.Formula

Get the type of formula.

getFreeWells() - Method in class net.sf.basedb.core.BioPlate

Get the number of free wells on this plate.

getFreeWells() - Method in class net.sf.basedb.core.data.BioPlateData

Get the number of wells that are free on the bioplate.

getFreezer() - Method in class net.sf.basedb.core.BioPlate

Gets the storage location of this bio plate

getFreezer() - Method in class net.sf.basedb.core.data.BioPlateData

Get the hardware, ie. freezer where the plate is kept.

getFriends() - Method in class net.sf.basedb.core.SessionControl

Get the id of all friends to logged in user.

getFrom() - Method in class net.sf.basedb.core.AnyToAny

Get the item this link is linking from.

getFrom() - Method in class net.sf.basedb.core.data.MessageData

The name of the user this message is from.

getFrom() - Method in class net.sf.basedb.core.Message

Get the name of the sender of this message.

getFromId() - Method in class net.sf.basedb.core.AnyToAny

Get the ID of the item this link is linking from.

getFromId() - Method in class net.sf.basedb.core.data.AnyToAnyData

The ID of the item we are linking from.

getFromId() - Method in class net.sf.basedb.core.data.MessageData

The id of the user if this message was from a real user.

getFromType() - Method in class net.sf.basedb.core.AnyToAny.FastLinkLoader

The source item type.

getFromType() - Method in class net.sf.basedb.core.AnyToAny

Get the type of the item this link is linking from.

getFromType() - Method in class net.sf.basedb.core.data.AnyToAnyData

The type code of the item we are linking from.

getFullClass(String...) - Method in class net.sf.basedb.clients.web.taglib.CalendarButton

Make sure that "auto-init" is added to the class attribute.

getFullClass(String...) - Method in class net.sf.basedb.clients.web.taglib.StylableTag

Get the full class (eg. main and subclass) as a single string.

getFullPermissionNames(Set<Permission>, String) - Static method in class net.sf.basedb.clients.web.PermissionUtil

Create a comma-separated string with "readable" permission names.

getFullPermissionNames(Identifiable) - Static method in class net.sf.basedb.clients.web.PermissionUtil

getFullQuotedTableName(DbEngine) - Method in class net.sf.basedb.core.dbengine.TableInfo

Get the fully quialified and quoted table name using the quoting rules from the given DBEngine

getFunctionName() - Method in class net.sf.basedb.util.jep.ChannelFunction

getFunctionName() - Method in class net.sf.basedb.util.jep.ExtraValueFunction

getFunctionName() - Method in class net.sf.basedb.util.jep.InReporterListFunction

getFunctionName() - Method in interface net.sf.basedb.util.jep.JepFunction

Get the name of this function.

getFunctionName() - Method in class net.sf.basedb.util.jep.LeftFunction

getFunctionName() - Method in class net.sf.basedb.util.jep.Log2Function

getFunctionName() - Method in class net.sf.basedb.util.jep.MeanFunction

getFunctionName() - Method in class net.sf.basedb.util.jep.NotInReporterListFunction

getFunctionName() - Method in class net.sf.basedb.util.jep.PositionFunction

getFunctionName() - Method in class net.sf.basedb.util.jep.RawChannelFunction

getFunctionName() - Method in class net.sf.basedb.util.jep.RawFunction

getFunctionName() - Method in class net.sf.basedb.util.jep.ReporterFunction

getFunctionName() - Method in class net.sf.basedb.util.jep.ScoreFunction

getFunctionName() - Method in class net.sf.basedb.util.jep.SimpleJepFunction

getFunctionName() - Method in class net.sf.basedb.util.parser.ColFunction

getFunctionName() - Method in class net.sf.basedb.util.parser.DataNoFunction

getFunctionName() - Method in class net.sf.basedb.util.parser.DefaultItemFunction

getFunctionName() - Method in class net.sf.basedb.util.parser.LineNoFunction

getFunctions() - Static method in class net.sf.basedb.util.jep.Jep

Get a list of built-in functions supported by the Jep.jepToExpression(JEP) converter.

getFutureResult(Callable<T>, QueryExecutor.Cancelable, SessionControl) - Static method in class net.sf.basedb.core.QueryExecutor

Run the callable and wait for the result.

getGenericDataFiles(DbControl, FileStoreEnabled, String) - Static method in class net.sf.basedb.core.FileStoreUtil

Get all files with a specific generic ItemSubtype in a given item's file set.

getGenericMembers(DbControl, FileStoreEnabled, String) - Static method in class net.sf.basedb.core.FileStoreUtil

Get all file members with a specific generic ItemSubtype in a given item's file set.

getGenericPlatformFileTypes(DbControl, FileStoreEnabled, String) - Static method in class net.sf.basedb.core.FileStoreUtil

Get a list of all platform file types that has the specified generic ItemSubtype.

getGenericType() - Method in class net.sf.basedb.core.data.DataFileTypeData

Get the generic file type of files with this member type.

getGenericType() - Method in class net.sf.basedb.core.DataFileType

Get the generic file type for this data file type.

getGetter() - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter

getGlobalSignalId() - Method in class net.sf.basedb.core.signal.AbstractSignalTransporter

Get the raw ID string that was passed to the AbstractSignalTransporter.init(String) method.

getGlobalSignalId(SignalHandler) - Method in class net.sf.basedb.core.signal.AbstractSignalReceiver

Generate a signal ID string.

getGlobalSignalId(SignalHandler) - Method in class net.sf.basedb.core.signal.SocketSignalReceiver

Override ID generation so we can add proxy information if needed.

getGranted() - Method in class net.sf.basedb.core.data.keyring.PluginKeys

Get the granted permissions.

getGranted() - Method in class net.sf.basedb.core.data.PluginPermission

The permissions for the plugin

getGranted(RoleKey) - Method in class net.sf.basedb.core.PluginDefinition

Get the permissions that have been granted to this plugin.

getGroup() - Method in class net.sf.basedb.core.data.DiskUsageData

Get the GroupData that owns the DiskConsumable item.

getGroup() - Method in class net.sf.basedb.core.DiskUsage

Get the group that owns the DiskConsumable item or null if ther is none.

getGroupId() - Method in class net.sf.basedb.core.data.keyring.GroupKeys

Get the id of the group.

getGroupId() - Method in class net.sf.basedb.core.data.keyring.GroupProjects

Get the id of the group.

getGroupId() - Method in class net.sf.basedb.core.data.keyring.UserGroups

Get the id of the group.

getGroupIds(Permission) - Method in class net.sf.basedb.core.ItemKey

Get the ID:s of all groups that have the specified permission in this item key.

getGroupPermissions() - Method in class net.sf.basedb.core.GroupPermissions

Get the internal representation of the permissions.

getGroups() - Method in class net.sf.basedb.core.data.ItemKeyData

Get the map that manages which groups that have permissions for this key.

getGroups() - Method in class net.sf.basedb.core.data.ProjectData

Get the map that manages which users are members of this project and their permissions.

getGroups() - Method in class net.sf.basedb.core.data.UserData

This is the inverse end.

getGroups() - Method in class net.sf.basedb.core.Group

Get a query that returns the groups that are members of this group.

getGroups() - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring

Return empty set.

getGroups() - Method in class net.sf.basedb.core.Job.SignalKeyring

Return empty set.

getGroups() - Method in class net.sf.basedb.core.MultiPermissions

Get a query that returns all groups appearing in at least one of the item keys.

getGroups() - Method in class net.sf.basedb.core.Project

Get a query that returns the groups that are members of this project.

getGroups() - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring

Return empty set.

getGroups() - Method in class net.sf.basedb.core.SessionControl

Get the id of all groups where the logged in user is a member, directly or indirectly.

getGroups() - Method in class net.sf.basedb.core.User

Get a query that returns the groups where this user is a member.

getGroups(boolean) - Method in class net.sf.basedb.core.Keyring

getGroupsRecursive(DbControl, Set<Integer>) - Static method in class net.sf.basedb.core.Group

Load all groups withing groups.

getGroupsRecursive(Session, Collection<Integer>) - Static method in class net.sf.basedb.core.Group

getGuiContext() - Method in class net.sf.basedb.clients.web.extensions.JspContext

Get the current GuiContext.

getGuiContext() - Method in class net.sf.basedb.core.PluginConfigurationRequest

Get the context of the client application when this configuration request was created.

getGuiContexts() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport

getGuiContexts() - Method in class net.sf.basedb.core.data.PluginDefinitionData

The item code for all items where it makes sense to use the plugin in a client application.

getGuiContexts() - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

getGuiContexts() - Method in interface net.sf.basedb.core.plugin.InteractivePlugin

Get a set containing all items that the plugin handles.

getGuiContexts() - Method in class net.sf.basedb.core.PluginDefinition

Get the Item types where it makes sense to use this plugin for a client application.

getGuiContexts() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter

This plug-in works in list context of all Annotatable items, except bioassay sets, bioassays and wells because they are not standalone items.

getGuiContexts() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin

getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

This plug-in works in list context of all Nameable items, except bioassay sets, bioassays and wells because they are not standalone items.

getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter

getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter

getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.ArraySlideImporter

getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.BioPlateImporter

getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.BioSourceImporter

getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.ExtractImporter

getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.FileImporter

getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.KitImporter

getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter

getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.SampleImporter

getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.TagImporter

getGuiContexts() - Method in class net.sf.basedb.plugins.BfsExporterPlugin

getGuiContexts() - Method in class net.sf.basedb.plugins.CdfFileReporterImporter

getGuiContexts() - Method in class net.sf.basedb.plugins.executor.AbstractIOSupport

getGuiContexts() - Method in class net.sf.basedb.plugins.FormulaFilter

getGuiContexts() - Method in class net.sf.basedb.plugins.GalExporter

getGuiContexts() - Method in class net.sf.basedb.plugins.HelpExporter

getGuiContexts() - Method in class net.sf.basedb.plugins.HelpImporter

getGuiContexts() - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter

getGuiContexts() - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin

getGuiContexts() - Method in class net.sf.basedb.plugins.JepExtraValueCalculator

getGuiContexts() - Method in class net.sf.basedb.plugins.JepIntensityTransformer

getGuiContexts() - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator

getGuiContexts() - Method in class net.sf.basedb.plugins.PackedFileExporter

getGuiContexts() - Method in class net.sf.basedb.plugins.PlateFlatFileImporter

getGuiContexts() - Method in class net.sf.basedb.plugins.PlateMappingExporter

Return a set containing the context:s [PLATEMAPPING, ITEM].

getGuiContexts() - Method in class net.sf.basedb.plugins.PlateMappingImporter

Return a set containing the context:s [PLATEMAPPING, LIST].

getGuiContexts() - Method in class net.sf.basedb.plugins.PluginConfigurationExporter

getGuiContexts() - Method in class net.sf.basedb.plugins.PluginConfigurationImporter

getGuiContexts() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter

getGuiContexts() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter

getGuiContexts() - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter

Return a set containing the context:s [REPORTER, LIST], [REPORTERLIST, ITEM], [REPORTERSCORE, LIST].

getGuiContexts() - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

Return a set containing the element [ARRAYDESIGN, ITEM].

getGuiContexts() - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker

getGuiTitle() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField

getGuiTitle() - Method in class net.sf.basedb.plugins.BfsExporterPlugin.ExtendedExportableField

getHandlerId() - Method in class net.sf.basedb.core.signal.AbstractSignalTransporter

Get the local handler ID part of the signal URI.

getHardware() - Method in class net.sf.basedb.core.BioMaterialEvent

Get the Hardware that was used in this event.

getHardware() - Method in class net.sf.basedb.core.BioPlateEvent

Get the Hardware that was used in this event.

getHardware() - Method in class net.sf.basedb.core.data.BioMaterialEventData

Get the hardware used in this event

getHardware() - Method in class net.sf.basedb.core.data.BioPlateEventData

Get the hardware used in this event

getHardware() - Method in class net.sf.basedb.core.data.DerivedBioAssayData

Get the hardware used to create this bioassay set.

getHardware() - Method in class net.sf.basedb.core.data.PlateEventData

Get the hardware used in this event.

getHardware() - Method in class net.sf.basedb.core.DerivedBioAssay

Get the Hardware that was used when creating this bioassay set.

getHardware() - Method in class net.sf.basedb.core.PlateEvent

Get the Hardware that was used in this event.

getHasData() - Method in class net.sf.basedb.core.data.RawBioAssayData

If the raw bioassay has data or not.

getHasFeatures() - Method in class net.sf.basedb.core.data.ArrayDesignData

If the array design has features or not.

getHashString(String) - Static method in class net.sf.basedb.util.MD5

Calculates the MD5 hash of an UTF-8 encoded string.

getHashString(MessageDigest) - Static method in class net.sf.basedb.util.MD5

getHeader(int) - Method in class net.sf.basedb.util.bfs.AnnotationModel

Get the column header for a given column index.

getHeader(String) - Method in class net.sf.basedb.core.RawBioAssay

Get the value for the raw data header with the specified name.

getHeader(String) - Method in class net.sf.basedb.util.parser.FlatFileParser

Get the value of the header with the specified name.

getHeaderAttribute(String, Pattern) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload

getHeaderNames() - Method in class net.sf.basedb.core.RawBioAssay

Get the names of all raw data headers.

getHeaderNames() - Method in class net.sf.basedb.util.parser.FlatFileParser

Get the names of all headers found by the FlatFileParser.parseHeaders() method.

getHeaders() - Method in class net.sf.basedb.core.data.RawBioAssayData

File headers from the raw data file.

getHeaders() - Method in class net.sf.basedb.util.bfs.AnnotationModel

Get all column headers.

getHeight() - Method in interface net.sf.basedb.clients.web.extensions.plot.PlotGenerator

Get the height of the generated image.

getHeight() - Method in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean

getHeight() - Method in class net.sf.basedb.core.AnnotationType

Get the recommended height in characters a client application should use to render an input field for annotations of this annotation type.

getHeight() - Method in class net.sf.basedb.core.data.AnnotationTypeData

The recommended height (lines) to display input fields for this annotation in client applications.

getHeight() - Method in class net.sf.basedb.core.ParameterType

Get the height of the input field for the parameter in the GUI.

getHelp() - Method in interface net.sf.basedb.clients.web.extensions.login.LoginFormAction

Optional help text that is displayed on the login form to aid the user when logging in.

getHelp() - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean

getHelp() - Method in class net.sf.basedb.clients.web.extensions.login.PasswordLoginFormFactory

getHelp() - Method in class net.sf.basedb.core.Client

Get a query that will return all help texts for this client.

getHelpByExternalId(DbControl, String, boolean) - Method in class net.sf.basedb.core.Client

Get a Help item when you know the external ID.

getHelpid() - Method in class net.sf.basedb.clients.web.taglib.Help

getHelpid() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab

getHelpId() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory

getHelpId() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab

getHelpId() - Method in interface net.sf.basedb.clients.web.extensions.tabcontrol.TabAction

The external id of a help text that the user can display to get more information about how to use the information in this tab.

getHelpId() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean

getHelpId() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab

getHelpTexts() - Method in class net.sf.basedb.core.data.ClientData

This is the inverse end.

getHibernateConfig() - Method in class net.sf.basedb.core.hibernate.SessionFactoryConfiguration

Deprecated.

Get the underlying Hibernate configuration instance.

getHibernateFlushMode() - Method in class net.sf.basedb.core.hibernate.QueryWrapper

getHibernateFlushMode() - Method in class net.sf.basedb.core.hibernate.SessionWrapper

getHibernateSession() - Method in class net.sf.basedb.core.DbControl

Get the underlying Hibernate session.

getHibernateType() - Method in class net.sf.basedb.core.hibernate.TypeWrapper

Get the underlying Hibernate type.

getHibernateType() - Method in class net.sf.basedb.core.Metadata.BasicData2ItemPropertyPath

getHibernateType() - Method in class net.sf.basedb.core.Metadata.BasicItem2DataPropertyPath

getHibernateType() - Method in class net.sf.basedb.core.Metadata.CollectionPropertyPath

getHibernateType() - Method in class net.sf.basedb.core.Metadata.CombinedPropertyPath

getHibernateType() - Method in class net.sf.basedb.core.Metadata.ComponentPropertyPath

getHibernateType() - Method in class net.sf.basedb.core.Metadata.DateCopyPropertyPath

getHibernateType() - Method in class net.sf.basedb.core.Metadata.EntityPropertyPath

getHibernateType() - Method in class net.sf.basedb.core.Metadata.EvictPropertyPath

getHibernateType() - Method in class net.sf.basedb.core.Metadata.IdentifierPropertyPath

getHibernateType() - Method in class net.sf.basedb.core.Metadata.MapPropertyPath

getHibernateType() - Method in class net.sf.basedb.core.Metadata.NoopPropertyPath

getHibernateType() - Method in interface net.sf.basedb.core.Metadata.PropertyPath

Get type information about the value that is returned by this path.

getHibernateType() - Method in class net.sf.basedb.core.Metadata.ReporterScore2DataPropertyPath

getHiddenFilteredColumns() - Method in class net.sf.basedb.clients.web.taglib.table.Table

getHiddenMembers() - Method in class net.sf.basedb.core.data.GroupData

A flag indicating if members of the group should be hidden to each other or not.

getHideclazz() - Method in class net.sf.basedb.clients.web.taglib.HideableSection

getHideClazz() - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory.Section

getHideClazz() - Method in interface net.sf.basedb.clients.web.extensions.section.SectionAction

Additional class attribute of the main section tag that is used when the section is hidden.

getHideClazz() - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean

getHighestScoreIdx(double[][]) - Method in class net.sf.basedb.util.fuzzy.StringMatcher

getHighlight() - Method in class net.sf.basedb.clients.web.taglib.table.Row

getHints() - Method in class net.sf.basedb.core.hibernate.QueryWrapper

getHistoryOf(BasicItem) - Static method in class net.sf.basedb.core.ChangeHistory

Get the history for a given item.

getHome() - Method in class net.sf.basedb.util.extensions.xml.PathConverter

Get the value of the home path.

getHome(Extension<?>) - Method in class net.sf.basedb.clients.web.extensions.JspContext

Get the URL to the home directory for a given extension.

getHomeDirectory() - Method in class net.sf.basedb.core.data.UserData

Get the home directory for this user.

getHomeDirectory() - Method in class net.sf.basedb.core.User

Get the home Directory for this user.

getHomeUrl(String) - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Get the URL to the home directory of extension with the given ID.

getHost() - Method in class net.sf.basedb.core.data.FileServerData

Get the name:port of the actual host to use for all files using this server (overrides the host specified in the file url)

getHost() - Method in class net.sf.basedb.core.FileServer

Get the name:port of the host that should override the host:port in the file url for files using this file server.

getHost() - Method in class net.sf.basedb.util.uri.ConnectionParameters

Get the host:port that should override the host:port specified by the file URI.

getHostName() - Static method in class net.sf.basedb.core.Application

Get the host name of the server running BASE.

getHref() - Method in class net.sf.basedb.clients.web.taglib.Icon

getHref() - Method in class net.sf.basedb.clients.web.taglib.path.PathElement

getHTML(ButtonAction, boolean, boolean) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarButtonRenderer

Generate the HTML that is needed to create a toolbar button.

getIcon() - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

getIcon() - Method in interface net.sf.basedb.clients.web.extensions.menu.MenuItemAction

Get an absolute reference to an image that will be displayed in the menu.

getIcon() - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean

getIcon() - Method in interface net.sf.basedb.clients.web.extensions.toolbar.ButtonAction

Get a reference to an image that will be displayed in the menu.

getIcon() - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean

getIcon() - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory

getIcon() - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem

getIcon() - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu

getIcon() - Method in class net.sf.basedb.clients.web.taglib.table.Button.ButtonActionWrapper

getIcon() - Method in enum class net.sf.basedb.util.extensions.logging.LogLevel

Get the icon that represents this log level.

getId() - Method in class net.sf.basedb.clients.jobagent.Agent

Get the agent.id configuration value.

getId() - Method in class net.sf.basedb.clients.jobagent.slotmanager.Slot

Get the id of the slot.

getId() - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup

The ID of the group.

getId() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

getId() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction

ID attribute of the column.

getId() - Method in interface net.sf.basedb.clients.web.extensions.login.LoginFormAction

Get the ID of this login form.

getId() - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean

getId() - Method in class net.sf.basedb.clients.web.extensions.login.PasswordLoginFormFactory

getId() - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

getId() - Method in interface net.sf.basedb.clients.web.extensions.menu.MenuItemAction

ID attribute of the main menu tag.

getId() - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean

getId() - Method in interface net.sf.basedb.clients.web.extensions.plot.OverviewPlotAction

The ID of the overview plots.

getId() - Method in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean

getId() - Method in interface net.sf.basedb.clients.web.extensions.plot.PlotGenerator

Get the ID of the image.

getId() - Method in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean

getId() - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory.Section

getId() - Method in interface net.sf.basedb.clients.web.extensions.section.SectionAction

ID attribute of the main section tag.

getId() - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean

getId() - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory

getId() - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory.MySkinAction

getId() - Method in interface net.sf.basedb.clients.web.extensions.skin.SkinAction

Get the ID of the extension.

getId() - Method in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory

getId() - Method in interface net.sf.basedb.clients.web.extensions.startpage.StartPageAction

Get the ID of the the action.

getId() - Method in class net.sf.basedb.clients.web.extensions.startpage.StartPageBean

getId() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory

getId() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab

getId() - Method in interface net.sf.basedb.clients.web.extensions.tabcontrol.TabAction

ID attribute of the main tab tag.

getId() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean

getId() - Method in interface net.sf.basedb.clients.web.extensions.toolbar.ButtonAction

ID attribute of the main button tag.

getId() - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean

getId() - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory

getId() - Method in class net.sf.basedb.clients.web.taglib.Button

getId() - Method in class net.sf.basedb.clients.web.taglib.table.Button.ButtonActionWrapper

getId() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn

getId() - Method in class net.sf.basedb.core.BasicItem

getId() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink

getId() - Method in class net.sf.basedb.core.data.BasicData

Get the id of the item.

getId() - Method in interface net.sf.basedb.core.data.IdentifiableData

Get the id for the item.

getId() - Method in class net.sf.basedb.core.data.UserData

We must override this method because the id must be the same as the id for the password.

getId() - Method in interface net.sf.basedb.core.Identifiable

Get the id for the item.

getId() - Method in class net.sf.basedb.core.ItemContext

Get the ID of the current item in this context.

getId() - Method in class net.sf.basedb.core.ItemProxy

getId() - Method in class net.sf.basedb.core.ParameterValuesImpl

getId() - Method in class net.sf.basedb.core.plugin.NamespaceParameterValuesWrapper

getId() - Method in interface net.sf.basedb.core.plugin.ParameterValues

Get the ID of the job or configuration the parameters comes from.

getId() - Method in class net.sf.basedb.core.plugin.ParameterValuesWrapper

Get the ID of either the job or the configuration, depending in the preferJob parameter that was set when creating this object.

getId() - Method in class net.sf.basedb.core.RawDataBatcher.FeatureProxy

getId() - Method in class net.sf.basedb.core.RawDataBatcher.ReporterProxy

getId() - Method in class net.sf.basedb.core.RawDataType

Get the id of this raw data type.

getId() - Method in class net.sf.basedb.core.SessionControl

Get the id of this SessionControl.

getId() - Method in class net.sf.basedb.core.signal.Signal

Get the signal ID.

getId() - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil

The ID of the annotation type that this loader load annotations from.

getId() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField

getId() - Method in class net.sf.basedb.plugins.BfsExporterPlugin.ExtendedExportableField

getId() - Method in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues

getId() - Method in interface net.sf.basedb.util.extensions.Extension

Get the ID of the extension.

getId() - Method in class net.sf.basedb.util.extensions.ExtensionBean

getId() - Method in interface net.sf.basedb.util.extensions.ExtensionPoint

Get the ID of the extension point.

getId() - Method in class net.sf.basedb.util.extensions.ExtensionPointBean

getId() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension

getId() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint

getId() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter.RawDataProxy

getId() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter.ReporterProxy

getId() - Method in class net.sf.basedb.util.importer.spotdata.ExtraFloatParser

Get the external id of the extra value type.

getId() - Method in interface net.sf.basedb.util.overview.extensions.ValidationRuleAction

Get the unique ID of this validation rule.

getId() - Method in class net.sf.basedb.util.overview.Node

Get a unique ID for this node.

getId() - Method in class net.sf.basedb.util.overview.Validator

Get the unique ID of this validator.

getId() - Method in interface net.sf.basedb.util.uri.ConnectionManagerFactory

Get the ID of this connection manager factory.

getId() - Method in class net.sf.basedb.util.uri.http.HttpConnectionManagerFactory

getId(String) - Static method in class net.sf.basedb.core.SystemItems

Get the numeric id for an item when you know the system id.

getId(BasicItem) - Method in class net.sf.basedb.clients.web.plugins.ItemQueryWrapper

Calls BasicItem.getId()

getId(BasicData) - Method in class net.sf.basedb.clients.web.plugins.DataQueryWrapper

Calls BasicData.getId()

getId(SqlResult) - Method in class net.sf.basedb.clients.web.plugins.DynamicQueryWrapper

Keeps a counter which is incremented at each call to this method.

getId(ReporterScore) - Method in class net.sf.basedb.clients.web.plugins.ReporterScoreQueryWrapper

Calls BasicData.getId().

getId(T) - Method in interface net.sf.basedb.clients.web.plugins.QueryWrapper

Get the ID of the specified item.

getIdentifier(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

getIdentifier(FeatureData) - Method in enum class net.sf.basedb.core.FeatureIdentificationMethod

Get the feature identifier for this method.

getIdentifier(RawData, String) - Method in enum class net.sf.basedb.core.FeatureIdentificationMethod

Get a feature identifier using this method

getIdFromPath(DbControl, Path) - Static method in class net.sf.basedb.core.Directory

Get the id of a directory when you know the path.

getIdHqlQuery(DbControl) - Method in class net.sf.basedb.core.AbstractHqlQuery

Build the ID query and set parameter values for it.

getIdMethod(DbControl, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Get the id method to use for finding items.

getIdMethod(DbControl, String) - Method in class net.sf.basedb.plugins.batchimport.FileImporter

We need to initialize the PathIdMethod when this is called.

getIdMethod(DbControl, Item, String) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter

getIdMethod(DbControl, Item, String) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Get an array with all identification methods that can be used to find items.

getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

Useable methods are: PropertyIdMethod.NAME PropertyIdMethod.EXTERNAL_ID InternalIdMethod.INTERNAL_ID FallbackIdMethod.NAME_OR_ID

getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter

Useable methods are: PropertyIdMethod.NAME InternalIdMethod.INTERNAL_ID FallbackIdMethod.NAME_OR_ID

getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter

Useable methods are: PropertyIdMethod.NAME InternalIdMethod.INTERNAL_ID FallbackIdMethod.NAME_OR_ID

getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.ArraySlideImporter

Useable methods are: PropertyIdMethod.NAME PropertyIdMethod.BARCODE InternalIdMethod.INTERNAL_ID FallbackIdMethod.NAME_OR_ID

getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.BioPlateImporter

Useable methods are: PropertyIdMethod.NAME PropertyIdMethod.BARCODE InternalIdMethod.INTERNAL_ID FallbackIdMethod.NAME_OR_ID

getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.BioSourceImporter

Useable methods are: PropertyIdMethod.NAME PropertyIdMethod.EXTERNAL_ID InternalIdMethod.INTERNAL_ID FallbackIdMethod.NAME_OR_ID

getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

Useable methods are: PropertyIdMethod.NAME InternalIdMethod.INTERNAL_ID FallbackIdMethod.NAME_OR_ID

getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.ExtractImporter

Useable methods are: PropertyIdMethod.NAME PropertyIdMethod.EXTERNAL_ID InternalIdMethod.INTERNAL_ID FallbackIdMethod.NAME_OR_ID

getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.FileImporter

Useable methods are: FileImporter.PathIdMethod InternalIdMethod.INTERNAL_ID

getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.KitImporter

Useable methods are: PropertyIdMethod.NAME InternalIdMethod.INTERNAL_ID FallbackIdMethod.NAME_OR_ID

getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter

Useable methods are: PropertyIdMethod.NAME InternalIdMethod.INTERNAL_ID FallbackIdMethod.NAME_OR_ID

getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

Useable methods are: PropertyIdMethod.NAME InternalIdMethod.INTERNAL_ID FallbackIdMethod.NAME_OR_ID

getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.SampleImporter

Useable methods are: PropertyIdMethod.NAME PropertyIdMethod.EXTERNAL_ID InternalIdMethod.INTERNAL_ID FallbackIdMethod.NAME_OR_ID

getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.TagImporter

Useable methods are: PropertyIdMethod.NAME InternalIdMethod.INTERNAL_ID FallbackIdMethod.NAME_OR_ID

getIdMethods(DbControl, Item) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter

getIdMethods(DbControl, Item) - Static method in class net.sf.basedb.plugins.batchimport.AnnotationIdMethod

Get identification methods that are based on annotations.

getIdMethods(DbControl, Item) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

getIdPrefix() - Method in class net.sf.basedb.clients.web.taglib.StylableTag

Optional prefix to include in the 'id' attribute.

getIdPrefix() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

getIdQuery(DbControl, boolean) - Method in class net.sf.basedb.core.AbstractQuery

Build a query string that is identical to the main query but only return the ID values.

getIgnoredFiles() - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Get files that are currently ignored.

getIgnoredFiles() - Method in class net.sf.basedb.util.extensions.manager.Settings

Get a list with all files that are ignored.

getIgnoredFiles(boolean) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager

Get all ignored files.

getIgnoredLines() - Method in class net.sf.basedb.util.parser.FlatFileParser

Get the number of lines that the last call to FlatFileParser.nextData() or FlatFileParser.hasMoreData() ignored because they matched the ignore regular expression.

getIgnoredSql() - Method in class net.sf.basedb.core.hibernate.SchemaGenerator

Get a list with the SQL statements that was ignored in the last run.

getIgnoreSubtypeFilter() - Method in class net.sf.basedb.core.ItemContext

getImage() - Method in class net.sf.basedb.clients.web.taglib.Button

getImage() - Method in class net.sf.basedb.clients.web.taglib.Help

getImage() - Method in class net.sf.basedb.clients.web.taglib.Icon

getImage() - Method in class net.sf.basedb.clients.web.taglib.table.Button

getImage() - Method in class net.sf.basedb.clients.web.taglib.table.Label

getImage() - Method in class net.sf.basedb.clients.web.taglib.Zoom

getImage() - Method in class net.sf.basedb.core.data.PlateMappingData

An optional name of a small image with a graphical representation of the mapping.

getImage() - Method in class net.sf.basedb.core.PlateMapping

Get the name of a small image that is a graphical representation of the mapping.

getImageRemapDir() - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory

getImpersonated() - Method in class net.sf.basedb.core.data.SessionData

Check if another user is acting as the user of this session.

getImpersonated() - Method in class net.sf.basedb.core.Session

Check if another user was acting as the user of this session.

getImpersonatedSessionControl(Job) - Method in class net.sf.basedb.clients.jobagent.Agent

Get a session control where the owner of the job has been impersonated and the active project has been set if needed.

getImplementingItems(Class<?>) - Static method in class net.sf.basedb.core.Metadata

Get all Item:s implementing/extinding the specified interface/class.

getImporter(DbControl, boolean, boolean) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

Get an instance of the importer plug-in.

getImportFileType() - Method in class net.sf.basedb.plugins.ManualTransformCreator

getInactiveRoles() - Method in class net.sf.basedb.core.Keyring

getInactiveRoles() - Method in class net.sf.basedb.core.SessionControl

Get the id of all inactive roles where the logged in user is a member.

getInclude() - Method in class net.sf.basedb.core.data.ContextData

Flags for specifying include options to an entity query.

getInclude() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData

Flags for specifying include options to an entity query.

getInclude() - Method in class net.sf.basedb.core.ItemContext

Get a Set object to specify Include options for a query.

getInclude() - Method in class net.sf.basedb.util.listable.TransformContext

Include options when executing queries to find parent/child items.

getIndex() - Method in class net.sf.basedb.core.BioPlateEventParticipant

Get the index of the plate in this event.

getIndex() - Method in class net.sf.basedb.core.data.BioPlateEventParticipantData

Get the index of this plate in the event.

getIndex() - Method in interface net.sf.basedb.util.extensions.Extension

The extensions in an extension point are by default ordered by their index value.

getIndex() - Method in class net.sf.basedb.util.extensions.ExtensionBean

getIndex() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension

getIndex(String) - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator

getIndex(String) - Method in class net.sf.basedb.core.DynamicResultIterator

getIndex(String) - Method in class net.sf.basedb.core.log.EntityDetails

Get the array index of the given property.

getIndex(String) - Method in interface net.sf.basedb.core.query.SqlResultIterator

Get the index number of a selected column.

getIndex(String) - Method in class net.sf.basedb.util.bfs.MetadataModel.Section

Get the index of the first entry with the given key.

getIndex(String, String[], Comparator<String>) - Method in class net.sf.basedb.core.Metadata

getIndexes() - Method in class net.sf.basedb.core.dbengine.TableInfo

Get information about the indexes in the table.

getInfo() - Method in class net.sf.basedb.clients.jobagent.AgentController

Get info about running job agent by sending an info request to the agents remote control service.

getInfo() - Method in class net.sf.basedb.core.JobAgent

Get info about the running job agent.

getInfo(boolean) - Method in class net.sf.basedb.util.jobagent.JobAgentConnection

Send an info or status request to the job agent.

getInheritedAnnotation(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

Get the parent annotation this annotation is inherited from.

getInheritedAnnotationColumns(String) - Static method in class net.sf.basedb.clients.web.Base

Get a query returning all annotation types that are needed to display inherited annotations for the given columns.

getInheritedAnnotationId() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

Get the ID of the annotation this annotation is inherited from.

getInheritedAnnotationSet(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

Get the annotation set this annotation is inherited from.

getInheritedAnnotationSetId() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

Get the ID of the annotation set this annotation is inherited from.

getInheritedFrom() - Method in class net.sf.basedb.core.Annotation

Get the parent annotation if this is an inherited or cloned annotation.

getInheritedFrom() - Method in class net.sf.basedb.core.data.AnnotationData

The parent annotation if this is an inherited or cloned annotation.

getInheritedFrom() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

Get a snapshot for the annotation this is inherited from.

getInheritingAnnotations() - Method in class net.sf.basedb.core.data.AnnotationData

Other annotations which inherit this annotation.

getInitial() - Method in class net.sf.basedb.clients.web.taglib.HideableSection

getInitializedFlatFileParser() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

Get an initialized parser that is configured by job or configuration values.

getInitializedFlatFileParser() - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter

Create a FlatFileParser that can parse Illumina data files: Data splitter: (,|\t) Header regexp: (.+)=(.*?)

getInitializedFlatFileParser() - Method in class net.sf.basedb.plugins.PlateMappingImporter

getInitializedFlatFileParser() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter

getInitializedFlatFileParser(InputStream, String) - Method in class net.sf.basedb.plugins.Base1PluginExecuter

Creates a FlatFileParser for a plugin configuration file.

getInitializedFlatFileParser(InputStream, String) - Method in class net.sf.basedb.util.basefile.BaseFileParser

Creates a FlatFileParser for parsing a BASEfile.

getInitializedFlatFileParser(ParameterValues) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

Create and initialise a flat file parser by setting all regular expressions and other options.

getInitParameter(String) - Method in class net.sf.basedb.clients.web.extensions.ServletWrapper

getInitParameterNames() - Method in class net.sf.basedb.clients.web.extensions.ServletWrapper

getInputStream() - Method in class net.sf.basedb.clients.web.fileupload.UploadedFile

Get an input stream for uploading the file.

getInputStream() - Method in class net.sf.basedb.util.importer.BaseFileWrapper

getInputStream() - Method in class net.sf.basedb.util.importer.DiskFileWrapper

getInputStream() - Method in interface net.sf.basedb.util.importer.FileWrapper

Get an input stream that reads data from the file.

getInputStream() - Method in interface net.sf.basedb.util.uri.ConnectionManager

Get an InputStream for reading the contents of the resource.

getInputStream() - Method in class net.sf.basedb.util.uri.http.HttpConnectionManager

getInputStream(long) - Method in class net.sf.basedb.util.uri.http.HttpConnectionManager

getInputStream(long) - Method in interface net.sf.basedb.util.uri.ResumableConnectionManager

Get an InputStream for reading the contents of the resource.

getInputStream(File) - Method in class net.sf.basedb.core.Migration

Get a stream for reading from the given file.

getInputStream(File) - Static method in class net.sf.basedb.util.FileUtil

Get a buffered InputStream object reading from the specified file.

getInputStream(String) - Method in class net.sf.basedb.util.bfs.BaseInputStreamLocator

Finds and opens an input stream to the file with the given filename.

getInputStream(String) - Method in class net.sf.basedb.util.bfs.DiskInputStreamLocator

Finds and opens an input stream to the file with the given filename.

getInputStream(String) - Method in interface net.sf.basedb.util.bfs.InputStreamLocator

Create an input stream that reads data from the given named resource.

getInputStream(String, int) - Method in class net.sf.basedb.util.StaticCache

Get a lock-safe input stream.

getInputStream(UploadedFile) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload

Get an input stream for reading from the current file section.

getInsertAutoIncrementSql(PersistentClass) - Method in interface net.sf.basedb.core.dbengine.DbEngine

Return a SQL fragment that can be used in an INSERT INTO statement to generate an ID for new rows.

getInsertAutoIncrementSql(PersistentClass) - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine

getInsertAutoIncrementSql(PersistentClass) - Method in class net.sf.basedb.core.dbengine.MySQLEngine

getInsertAutoIncrementSql(PersistentClass) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine

getInsertPropertyOrder(Class<? extends BatchableData>) - Static method in class net.sf.basedb.core.BatchUtil

Get the order of properties in the insert SQL.

getInsertPropertyOrder(String) - Static method in class net.sf.basedb.core.BatchUtil

Get the order of properties in the insert SQL.

getInsertSql(Class<? extends BatchableData>) - Static method in class net.sf.basedb.core.BatchUtil

Get the SQL that inserts a new row of the specified class.

getInsertSql(String) - Static method in class net.sf.basedb.core.BatchUtil

Get the SQL that inserts a new row of the specified class.

getInstalledFiles() - Method in class net.sf.basedb.util.extensions.manager.Settings

Get a list with all files that are installed.

getInstalledSchemaVersion() - Method in class net.sf.basedb.core.hibernate.SessionFactoryConfiguration

Deprecated.

Get the schema version that was installed prior to updating it.

getInstalledSchemaVersion() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration

Get the currently installed version of the schema or 0 if not installed.

getInstallMode() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration

Get the installation mode that BASE will use when creating the session factory.

getInstance() - Static method in class net.sf.basedb.util.jep.Log2Function

Get the singleton instance of this function.

getInstance(Class<I>) - Static method in class net.sf.basedb.core.Metadata

Get the metadata instance for the specified type of item.

getInstance(Class<I>, String) - Static method in class net.sf.basedb.core.Metadata

Get the metadata instance for the item with the specified entity name.

getInstance(String) - Static method in class net.sf.basedb.core.authentication.AuthenticationMethod

Get an instance of this class for the given authentication method.

getInstance(String) - Static method in class net.sf.basedb.util.JarClassLoader

Get a class loader for the specified JAR file.

getInstance(String, boolean) - Static method in class net.sf.basedb.util.JarClassLoader

Get a class loader for the specified JAR file, optionally unloading an the old one if the JAR file has been modified.

getInstanceIfEnabled(SessionControl) - Static method in class net.sf.basedb.core.log.db.DbLogManagerFactory

Get the current database log manager factory if database logging is enabled.

getInt(int) - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult

getInt(int) - Method in class net.sf.basedb.core.DynamicResultIterator.SqlResultImpl

getInt(int) - Method in interface net.sf.basedb.core.query.SqlResult

Get the value of the specified column as an integer.

getInt(int) - Method in class net.sf.basedb.util.parser.FlatFileParser.Data

Shortcut for getInt(index, null, true)

getInt(int, NumberFormat, boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser.Data

Get the value as an integer.

getInt(int, NumberFormat, boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser.ExcelData

getInt(Integer) - Static method in class net.sf.basedb.core.IntegerUtil

Get the value of an Integer.

getInt(Integer, int) - Static method in class net.sf.basedb.core.IntegerUtil

Get the value of an Integer.

getInt(String) - Static method in class net.sf.basedb.core.Config

Get the configuration setting specified by key as an integer value.

getInt(String) - Static method in class net.sf.basedb.core.IntegerUtil

Get the int value of an String.

getInt(String) - Static method in class net.sf.basedb.util.Values

Convert a string to an integer.

getInt(String[]) - Static method in class net.sf.basedb.util.Values

Convert an array of strings to an array of Integer:s.

getInt(String, int) - Static method in class net.sf.basedb.core.Config

Get the configuration setting specified by key as an integer value.

getInt(String, int) - Static method in class net.sf.basedb.core.IntegerUtil

Get the int value of an String.

getInt(String, int) - Static method in class net.sf.basedb.util.Values

Convert a string to an integer.

getInt(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.ColumnMapper

getInt(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.CompoundMapper

getInt(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.ConstantMapper

getInt(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.CropStringMapper

getInt(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.JepMapper

getInt(FlatFileParser.Data) - Method in interface net.sf.basedb.util.parser.Mapper

Get the value for the line of data as an integer.

getInt(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.NullIfExceptionMapper

getIntAttribute(Element, String, int) - Static method in class net.sf.basedb.util.XmlUtil2

Get the value of an attribute as an integer.

getIntCellStyle() - Method in class net.sf.basedb.util.excel.CellStyleCreator

Get the cell style for formatting numbers without decimals.

getInteger(String, Integer) - Static method in class net.sf.basedb.util.Values

getIntegerValues() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink

getIntensityField(String, String) - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter

Create a dynamic field for spot intensity if the field name has the pattern 'Ch X' where 'X' is a channel number between 1 and the number of channels in the raw data type used by the source bioassay set.

getIntensityField(String, String) - Method in class net.sf.basedb.util.export.spotdata.Base1FieldConverter

Create a dynamic field for spot intensity if the field name has the pattern 'intensityX' where 'X' is a channel number between 1 and the number of channels in the raw data type used by the source bioassay set.

getIntensityFormula(String) - Method in class net.sf.basedb.core.RawDataType

getIntensityFormulas() - Method in class net.sf.basedb.core.RawDataType

getIntensityTransform() - Method in class net.sf.basedb.core.BioAssaySet

Get information about in what way the spot intensities has been transformed before they were stored in the database.

getIntensityTransform() - Method in class net.sf.basedb.core.data.BioAssaySetData

A flag indicating how the spot intensities has been transformed before it was stored in the database: 0 = no transformation; 1 = 2-log; 2 = 10-log

getIntensityTransform() - Method in class net.sf.basedb.core.DynamicQuery

Get the intensity transform that was used to store spot intensities for the root bioassay set in this query.

getIntensityTransform() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter

Get the intensity transform

getInterfaceName() - Method in class net.sf.basedb.core.data.PluginTypeData

Get the interface name a plugin must implement to be of this type.

getInterfaceName() - Method in class net.sf.basedb.core.PluginType

Get the class name of the Java class that implements this plugin.

getInterfaces(Class<?>) - Static method in class net.sf.basedb.util.ClassUtil

Get all interfaces a class implements, including those implemented by superclasses.

getInternalId() - Method in class net.sf.basedb.core.authentication.AuthenticatedUser

Get the internal id for the user (0 if not known)

getInternalId() - Method in class net.sf.basedb.util.extensions.xml.PluginInfo

Get the internal if of this plug-in.

getInternalName() - Method in class net.sf.basedb.core.data.FileData

Get the internal name accosiated with this file.

getInternalName() - Method in class net.sf.basedb.core.File

Get the internal name of this file.

getIntFormatter(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory

Get the logged in user's formatter for integral numbers.

getIntOption(String, Integer) - Method in class net.sf.basedb.core.AnnotationType

Get an option and convert the value to an integer.

getInvoker() - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerUtil

Get the invoker that is handling the extensions.

getInvoker(DbControl) - Method in class net.sf.basedb.core.FileSet

getInvoker(ClientContext, ExtensionsFilter) - Static method in class net.sf.basedb.util.uri.ConnectionManagerUtil

Get an invoker for using the connection manager factory extensions.

getInvoker(Extension<ServiceControllerAction>) - Static method in class net.sf.basedb.clients.web.extensions.service.Services

getItem() - Method in class net.sf.basedb.clients.web.taglib.PropertyValue

getItem() - Method in class net.sf.basedb.clients.web.taglib.SubtypeSelector

getItem() - Method in class net.sf.basedb.clients.web.taglib.table.Table

getItem() - Method in class net.sf.basedb.core.AnnotationSet

Get the item this annotation set belongs to.

getItem() - Method in class net.sf.basedb.core.ContextKey

getItem() - Method in class net.sf.basedb.core.DiskUsage

Get the item this disk usage holds information for

getItem() - Method in class net.sf.basedb.core.FileSet

Get the item this file set belongs to.

getItem() - Method in class net.sf.basedb.core.log.ManualLogEntry

Get the item this log entry is related to.

getItem() - Method in class net.sf.basedb.core.plugin.GuiContext

getItem() - Method in class net.sf.basedb.util.overview.Fix

Get the item that needs to be edited for this fix.

getItem() - Method in class net.sf.basedb.util.overview.Node

Get the item that is related to this node.

getItem(Class<I>, BasicData, Object...) - Method in class net.sf.basedb.core.DbControl

Get an item object for a known data object, using the cache if possible.

getItem(DbControl) - Method in class net.sf.basedb.core.AnnotationSet

Get the item this annotation set belongs to using a specific DbControl for database access.

getItem(DbControl) - Method in class net.sf.basedb.core.ChangeHistory

Load the item that was changed.

getItem(DbControl) - Method in class net.sf.basedb.core.ItemProxy

getItem(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot

Get item the annotations belong to.

getItem(DbControl) - Method in class net.sf.basedb.util.overview.Node

Get the item that is related to this node and make sure that it is loaded with the current DbControl.

getItem(DbControl, ChangeHistory, boolean, boolean) - Static method in class net.sf.basedb.clients.web.ChangeHistoryUtil

Get the item that was changed in HTML format.

getItemClass() - Method in enum class net.sf.basedb.core.Item

Get the class object that is used to handle items of this type.

getItemCount() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramSeries

getItemCount(int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset

getItemForAnnotationTypes() - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Does the importer want to use annotation types as identifiers importing?

getItemForAnnotationTypes() - Method in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter

Enable annotations as item identifier.

getItemForAnnotationTypes() - Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter

Enable annotations as item identifier.

getItemForAnnotationTypes() - Method in class net.sf.basedb.plugins.batchimport.ArraySlideImporter

Enable annotations as item identifier.

getItemForAnnotationTypes() - Method in class net.sf.basedb.plugins.batchimport.BioPlateImporter

Enable annotations as item identifier.

getItemForAnnotationTypes() - Method in class net.sf.basedb.plugins.batchimport.BioSourceImporter

Enable annotations as item identifier.

getItemForAnnotationTypes() - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

Enable annotations as item identifier.

getItemForAnnotationTypes() - Method in class net.sf.basedb.plugins.batchimport.ExtractImporter

Enable annotations as item identifier.

getItemForAnnotationTypes() - Method in class net.sf.basedb.plugins.batchimport.KitImporter

Enable annotations as item identifier.

getItemForAnnotationTypes() - Method in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter

Enable annotations as item identifier.

getItemForAnnotationTypes() - Method in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

Enable annotations as item identifier.

getItemForAnnotationTypes() - Method in class net.sf.basedb.plugins.batchimport.SampleImporter

Enable annotations as item identifier.

getItemForAnnotationTypes() - Method in class net.sf.basedb.plugins.batchimport.TagImporter

Enable annotations as item identifier.

getItemForSubtypes() - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Does the importer want to use item subtypes when importing?

getItemForSubtypes() - Method in class net.sf.basedb.plugins.batchimport.BioSourceImporter

getItemForSubtypes() - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

getItemForSubtypes() - Method in class net.sf.basedb.plugins.batchimport.ExtractImporter

getItemForSubtypes() - Method in class net.sf.basedb.plugins.batchimport.FileImporter

getItemForSubtypes() - Method in class net.sf.basedb.plugins.batchimport.KitImporter

getItemForSubtypes() - Method in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter

getItemForSubtypes() - Method in class net.sf.basedb.plugins.batchimport.SampleImporter

getItemForSubtypes() - Method in class net.sf.basedb.plugins.batchimport.TagImporter

getItemId() - Method in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo

Get the id of the current item.

getItemId() - Method in class net.sf.basedb.core.AnnotationSet

Get the ID of the item this annotation set belongs to.

getItemId() - Method in class net.sf.basedb.core.ChangeHistory

Get the ID of the item that was changed.

getItemId() - Method in class net.sf.basedb.core.data.AnnotationSetData

The ID if the item this annotation set is associated with.

getItemId() - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData

The ID of the item that was changed

getItemId() - Method in class net.sf.basedb.core.data.ContextData

Get the current item ID or 0 if no item is current.

getItemId() - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot

Get the ID of the item the annotations in this snapshot belong to.

getItemKey() - Method in interface net.sf.basedb.core.data.ShareableData

Get the ItemKeyData for the item.

getItemKey() - Method in class net.sf.basedb.core.data.SharedData

getItemKey() - Method in interface net.sf.basedb.core.Shareable

Get the ItemKey that is used to share this item to users and groups.

getItemKey() - Method in class net.sf.basedb.core.SharedItem

getItemKeyId() - Method in class net.sf.basedb.core.SessionControl

Get the id of the ItemKey that new items should be shared to according to the settings in the currently active project.

getItemKeys() - Method in class net.sf.basedb.core.data.GroupData

This is the inverse end.

getItemKeys() - Method in class net.sf.basedb.core.data.UserData

This is the inverse end.

getItemKeys() - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring

Return empty set.

getItemKeys() - Method in class net.sf.basedb.core.Job.SignalKeyring

Return empty set.

getItemKeys() - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring

Return empty set.

getItemKeys() - Method in class net.sf.basedb.core.SessionControl

Get the id of all item keys where the logged in user has read permission.

getItemKeys(Permission) - Method in class net.sf.basedb.core.Keyring

getItemKeys(Permission) - Method in class net.sf.basedb.core.SessionControl

Get the id of all item keys where the logged in user has the requested permission.

getItemList() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData

Get the item list this sync filter belongs to.

getItemList() - Method in class net.sf.basedb.core.SyncFilter

Get the item list this filter belongs to.

getItemListFromContext(DbControl, GuiContext) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter

If the current context is the "Members" tab for an item list we load the item list and will later require that all items to be annotated are members of that list.

getItemListFromContext(DbControl, GuiContext) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

If the current context is the "Members" tab for an item list we load the item list and will later require that all items to be annotated are members of that list.

getItemListFromContext(DbControl, GuiContext) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

If the current context is the "Members" tab for an item list we load the item list and will later require that all items to be linked are members of that list.

getItemListsEnum(DbControl, ItemContext, Filter<? super ItemList>) - Static method in class net.sf.basedb.clients.web.Base

Get available item lists as an Enumeration that is suitable to use in a column definition for a table.

getItemListsEnum(DbControl, Item, Collection<Include>) - Static method in class net.sf.basedb.clients.web.Base

Get available item lists as an Enumeration that is suitable to use in a column definition for a table.

getItemListsEnum(DbControl, Item, Collection<Include>, Filter<? super ItemList>) - Static method in class net.sf.basedb.clients.web.Base

Get available item lists as an Enumeration that is suitable to use in a column definition for a table.

getItemPermission() - Method in class net.sf.basedb.core.AbstractEntityQuery

getItemPermission() - Method in class net.sf.basedb.core.ItemContext

The permission the logged in user must have for items returned by a query.

getItemPermission() - Method in interface net.sf.basedb.core.query.EntityQuery

The logged in user's permission on the items returned by this query.

getItems() - Method in class net.sf.basedb.core.MultiPermissions

Returns the items that are handled within this class.

getItems() - Method in class net.sf.basedb.core.ParameterType

Get the list of values to choose from.

getItems(Collection<Item>) - Method in class net.sf.basedb.core.MultiPermissions

Get all items of specific item types.

getItems(Set<Item>, int, int, Permission, Set<Include>, Restriction) - Method in class net.sf.basedb.core.Project

Load the items in a project.

getItems(Set<Item>, int, int, Permission, Restriction) - Method in class net.sf.basedb.core.User

Load the items owned by this user.

getItems(DbControl, Set<Item>, int, int) - Static method in class net.sf.basedb.core.Trashcan

getItems(DbControl, Set<Item>, int, int, Restriction) - Static method in class net.sf.basedb.core.Trashcan

Load all items flagged for deletion that are owned by or removed by the logged in user.

getItems(DbControl, Item, int, int) - Static method in class net.sf.basedb.core.Trashcan

getItems(DbControl, ItemQuery<T>, Restriction...) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter

Sort the items by name and add USE permission filter to the query.

getItems(Item) - Method in class net.sf.basedb.core.MultiPermissions

Get all items of a specific item type.

getItems(Item, int, int, Permission) - Method in class net.sf.basedb.core.User

getItems(Item, int, int, Permission, Set<Include>) - Method in class net.sf.basedb.core.Project

getItemSubtype() - Method in class net.sf.basedb.clients.web.SubContext

The new item subtype.

getItemSubtype() - Method in class net.sf.basedb.core.AnnotationTypeCategory

Get the item subtype that is linked to this category of annotations.

getItemSubtype() - Method in class net.sf.basedb.core.BioMaterial

getItemSubtype() - Method in class net.sf.basedb.core.BioPlateType

Get the subtype that biomaterial items should have when placed on a plate with this bioplate type.

getItemSubtype() - Method in class net.sf.basedb.core.data.AnnotationTypeCategoryData

The subtype that is linked to this category of annotations.

getItemSubtype() - Method in class net.sf.basedb.core.data.BioMaterialData

getItemSubtype() - Method in class net.sf.basedb.core.data.BioPlateTypeData

Get the subtype of biomaterials that can be placed on plates of this type.

getItemSubtype() - Method in class net.sf.basedb.core.data.ContextData

Get the subtype of items that is associated with this context.

getItemSubtype() - Method in class net.sf.basedb.core.data.DerivedBioAssayData

getItemSubtype() - Method in class net.sf.basedb.core.data.FileData

getItemSubtype() - Method in class net.sf.basedb.core.data.HardwareData

getItemSubtype() - Method in class net.sf.basedb.core.data.ItemListData

Get the subtype of items that can be members in this list.

getItemSubtype() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData

Subtype context filter.

getItemSubtype() - Method in class net.sf.basedb.core.data.ItemSubtypeFileTypeData

Get the item subtype.

getItemSubtype() - Method in class net.sf.basedb.core.data.JobData

getItemSubtype() - Method in class net.sf.basedb.core.data.KitData

getItemSubtype() - Method in class net.sf.basedb.core.data.PhysicalBioAssayData

getItemSubtype() - Method in class net.sf.basedb.core.data.ProtocolData

getItemSubtype() - Method in class net.sf.basedb.core.data.SoftwareData

getItemSubtype() - Method in interface net.sf.basedb.core.data.SubtypableData

Get the subtype of the item.

getItemSubtype() - Method in class net.sf.basedb.core.data.TagData

getItemSubtype() - Method in class net.sf.basedb.core.DerivedBioAssay

getItemSubtype() - Method in class net.sf.basedb.core.Extract

getItemSubtype() - Method in class net.sf.basedb.core.File

getItemSubtype() - Method in class net.sf.basedb.core.Hardware

getItemSubtype() - Method in class net.sf.basedb.core.ItemList

Get the subtype of items that can be members in this list.

getItemSubtype() - Method in class net.sf.basedb.core.ItemSubtype

getItemSubtype() - Method in class net.sf.basedb.core.ItemSubtypeFileType

Get the item subtype.

getItemSubtype() - Method in class net.sf.basedb.core.Job

getItemSubtype() - Method in class net.sf.basedb.core.Kit

getItemSubtype() - Method in class net.sf.basedb.core.MeasuredBioMaterial

getItemSubtype() - Method in class net.sf.basedb.core.PhysicalBioAssay

getItemSubtype() - Method in class net.sf.basedb.core.Protocol

getItemSubtype() - Method in class net.sf.basedb.core.Sample

getItemSubtype() - Method in class net.sf.basedb.core.Software

getItemSubtype() - Method in interface net.sf.basedb.core.Subtypable

Get the subtype of the item.

getItemSubtype() - Method in class net.sf.basedb.core.SyncFilter

Get the subtype that items must match.

getItemSubtype() - Method in class net.sf.basedb.core.Tag

getItemSubtype() - Method in class net.sf.basedb.util.annotations.InheritSpecification

getItemSubtype(DbControl) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

getItemSubtype(DbControl) - Method in class net.sf.basedb.core.ItemContext

Get the subtype that is related to this context.

getItemSubtypes() - Method in class net.sf.basedb.core.data.DataFileTypeData

The subtypes that this file type can be used with.

getItemSubtypes() - Method in class net.sf.basedb.core.DataFileType

Get a query returning the item subtypes that files of this type can be used on.

getItemtype() - Method in class net.sf.basedb.clients.web.taglib.SubtypeSelector

getItemType() - Method in class net.sf.basedb.core.AbstractEntityQuery

getItemType() - Method in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo

Get the item type of the item.

getItemType() - Method in class net.sf.basedb.core.AnnotationSet

Get the Item type of the item this annotation set belongs to.

getItemType() - Method in class net.sf.basedb.core.ChangeHistory

Get the type of the item that was changed.

getItemType() - Method in class net.sf.basedb.core.data.AnnotationSetData

Get the item type this annotation set is associated with.

getItemType() - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData

The type code of the item that was changed.

getItemType() - Method in class net.sf.basedb.core.data.ContextData

Get the item type this context is valid for.

getItemType() - Method in class net.sf.basedb.core.data.ContextIndex

getItemType() - Method in class net.sf.basedb.core.data.DataFileTypeData

The item type this file type can be associated with.

getItemType() - Method in class net.sf.basedb.core.data.DiskUsageData

Get the item type this annotation set is associated with.

getItemType() - Method in class net.sf.basedb.core.data.FileSetData

Get the item type this file set is associated with.

getItemType() - Method in class net.sf.basedb.core.data.GuiContextData

getItemType() - Method in class net.sf.basedb.core.data.ItemSubtypeData

Get the item type this subtype can be applied to.

getItemType() - Method in class net.sf.basedb.core.data.RoleKeyData

Get the code for the type of items this role key applies to.

getItemType() - Method in class net.sf.basedb.core.DataFileType

Get the type of item files of this type can be used on.

getItemType() - Method in class net.sf.basedb.core.DataResultIterator

Get the type of items contained in this list.

getItemType() - Method in class net.sf.basedb.core.DiskUsage

Get the Item type of the item this annotation set belongs to.

getItemType() - Method in class net.sf.basedb.core.FileSet

Get the Item type of the item this file set belongs to.

getItemType() - Method in class net.sf.basedb.core.ItemContext

Get the type of item this object is storing context for.

getItemType() - Method in class net.sf.basedb.core.ItemResultIterator

Get the type of items contained in this list.

getItemType() - Method in class net.sf.basedb.core.ItemResultList

Get the type of items contained in this list.

getItemType() - Method in class net.sf.basedb.core.plugin.Permissions

Get the item type the permissions are valid for.

getItemType() - Method in interface net.sf.basedb.core.query.EntityQuery

The type of items the query returns.

getItemType() - Method in class net.sf.basedb.core.query.HqlEntityParameterExpression

Get the type of entites that are accepted by the parameter.

getItemType() - Method in class net.sf.basedb.core.query.QueryParameter

The parameter should be an entity of the given item type.

getItemType() - Method in class net.sf.basedb.core.ReporterScoreResultIterator

Get the type of items contained in this list.

getItemType() - Method in class net.sf.basedb.core.RoleKey

Get the Item type for the type of items this role key applies to.

getItemType() - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot

Get the item type of the item the annotations in this snapshot belong to.

getItemType() - Method in class net.sf.basedb.util.overview.Node

Get the item type of the item that this node related to this node.

getItemTypes() - Method in class net.sf.basedb.core.data.AnnotationTypeData

The item code for all items this annotation type can be applied to.

getItemValue(DbControl, Object) - Static method in class net.sf.basedb.core.Values

Convert a a data value to a item value.

getItemValues(DbControl, List<?>) - Static method in class net.sf.basedb.core.Values

Convert a list of data values to item values.

getJarFile() - Method in class net.sf.basedb.core.data.PluginDefinitionData

Get the file name of the JAR file where the plugin class is located.

getJarFile() - Method in class net.sf.basedb.core.data.PluginTypeData

Get the file name of the JAR file where the plugin class is located.

getJarFile() - Method in class net.sf.basedb.core.PluginDefinition

Get the name of the JAR file that contains this plug-in.

getJarFile() - Method in class net.sf.basedb.core.PluginType

Get the name of the JAR file that contains this plug-in.

getJarPath() - Method in class net.sf.basedb.core.PluginDefinition

Get the path to the JAR file that contains the plugin class file.

getJarPath() - Method in class net.sf.basedb.core.PluginType

Get the path to the JAR file that contains the plugin class file.

getJdbcBatchSize() - Method in class net.sf.basedb.core.hibernate.SessionWrapper

getJdbcBatchSize() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

getJdbcFetchSize() - Static method in class net.sf.basedb.core.HibernateUtil

The number of rows to load at a time when reading from the database.

getJep() - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField

Get the configured JEP expression.

getJepExpression() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn

getJepFunctions(DbControl, boolean) - Method in class net.sf.basedb.core.AbstractSqlQuery

Create custom JEP function that can be used with the current query.

getJepFunctions(DbControl, boolean) - Method in class net.sf.basedb.core.DataCube.RawMappingQuery

No JEP functions can be used with this type of query.

getJepFunctions(DbControl, boolean) - Method in class net.sf.basedb.core.DynamicExtraValueQuery

The following JEP functions can be used: pos(): PositionFunction

getJepFunctions(DbControl, boolean) - Method in class net.sf.basedb.core.DynamicPositionQuery

The following JEP function can be used: pos(): PositionFunction rep(property): ReporterFunction score(reporter-list-id): ScoreFunction xtra(extra-value-id): ExtraValueFunction (if a bioassay set has been specified) inList(reporter-list-id): InReporterListFunction (only if restrictions=true) notInList(reporter-list-id): NotInReporterListFunction (only if restrictions=true)

getJepFunctions(DbControl, boolean) - Method in class net.sf.basedb.core.DynamicRawDataQuery

getJepFunctions(DbControl, boolean) - Method in class net.sf.basedb.core.DynamicReporterQuery

The following JEP functions can be used: rep(property): ReporterFunction mrep(property): ReporterFunction (only for cloned reporters) inList(reporter-list-id): InReporterListFunction (only if restrictions=true) notInList(reporter-list-id): NotInReporterListFunction (only if restrictions=true)

getJepFunctions(DbControl, boolean) - Method in class net.sf.basedb.core.DynamicSpotQuery

The following JEP functions can be used: ch(n): ChannelFunction rawCh(n): RawChannelFunction pos(): PositionFunction rep(property): ReporterFunction score(reporter-list-id): ScoreFunction xtra(extra-value-id): ExtraValueFunction (if a bioassay set has been specified) raw(property): RawFunction inList(reporter-list-id): InReporterListFunction (only if restrictions=true) notInList(reporter-list-id): NotInReporterListFunction (only if restrictions=true)

getJob() - Method in class net.sf.basedb.core.ArrayDesign

Get the job that imported features to this array design.

getJob() - Method in class net.sf.basedb.core.data.ArrayDesignData

Get the job that was used to import features to this array desing

getJob() - Method in class net.sf.basedb.core.data.ChangeHistoryData

getJob() - Method in class net.sf.basedb.core.data.DerivedBioAssayData

Get the job used to create this bioassay set.

getJob() - Method in class net.sf.basedb.core.data.ExtraValueData

Get the job that was used to execute this calculate this extra value.

getJob() - Method in class net.sf.basedb.core.data.MessageData

If this message is a message about a job completion (or failure) this property contains a reference to that job.

getJob() - Method in class net.sf.basedb.core.data.RawBioAssayData

Get the job that was used to import raw data to this raw bioassay

getJob() - Method in class net.sf.basedb.core.data.TransformationData

Get the job that was used to execute this transformation

getJob() - Method in class net.sf.basedb.core.DerivedBioAssay

Get the job that created this bioassay.

getJob() - Method in class net.sf.basedb.core.ExtraValue

Get the job that created the extra values.

getJob() - Method in class net.sf.basedb.core.InternalJobQueue.JobRunner

Get the job.

getJob() - Method in class net.sf.basedb.core.Message

Get the Job this message is about.

getJob() - Method in class net.sf.basedb.core.ParameterValuesImpl

getJob() - Method in class net.sf.basedb.core.plugin.NamespaceParameterValuesWrapper

getJob() - Method in interface net.sf.basedb.core.plugin.ParameterValues

Get the job that we are executing/configuring.

getJob() - Method in class net.sf.basedb.core.plugin.ParameterValuesWrapper

getJob() - Method in class net.sf.basedb.core.PluginRequest

Get the job for the request or null if we are not configuring/executing a job.

getJob() - Method in class net.sf.basedb.core.RawBioAssay

Get the job that created or imported data to this raw bioassay.

getJob() - Method in class net.sf.basedb.core.Transformation

Get the job that executed this transformation.

getJob() - Method in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues

getJob(DbControl) - Method in class net.sf.basedb.core.ChangeHistory

Load the job that was executing when the change was made.

getJob(DbControl) - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo

Load the job that was executing the transaction.

getJob(DbControl, ChangeHistory, boolean, boolean) - Static method in class net.sf.basedb.clients.web.ChangeHistoryUtil

Get the job that made the change in HTML format.

getJobAgent() - Method in class net.sf.basedb.core.data.JobAgentSettingsData

The job agent these settings belong to.

getJobAgent() - Method in class net.sf.basedb.core.Job

Get the job agent this job should run on, is running on or was running on.

getJobAgent() - Method in class net.sf.basedb.core.JobAgentSettings

Get the job agent that owns these settings.

getJobAgent(DbControl) - Method in class net.sf.basedb.clients.jobagent.Agent

Get the JobAgent item corresponding to this agent.

getJobAgentId() - Method in class net.sf.basedb.core.data.JobData

The ID of the job agent this job should run/is running/was running on.

getJobAgentSettings() - Method in class net.sf.basedb.core.data.PluginDefinitionData

This is the inverse end.

getJobExecutorClass(String) - Method in class net.sf.basedb.clients.jobagent.Agent

Get the class object for the configured job executor.

getJobId() - Method in class net.sf.basedb.core.ChangeHistory

Get the ID of the job that was executing when the change was made

getJobId() - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo

Get the ID of the job that was executing the transaction.

getJobId() - Method in class net.sf.basedb.core.data.ChangeHistoryData

The ID of the job that was making the changes.

getJobId() - Method in class net.sf.basedb.core.log.TransactionDetails

Get the ID of the currently running job or 0 if no job is running.

getJobId() - Method in class net.sf.basedb.core.SessionControl

Get the id of the job that is currently running with this session control.

getJobId() - Method in class net.sf.basedb.util.jobagent.JobInfo

Get the ID of the job.

getJobInfo() - Method in class net.sf.basedb.util.jobagent.JobAgentInfo

Get detailed information about the running jobs.

getJobName() - Method in class net.sf.basedb.core.log.TransactionDetails

Utility method for loading the name of the currently executing job.

getJobName() - Method in class net.sf.basedb.core.SessionControl

Get the name of the job that is currently running with this session control.

getJobOrConfigurationValue(String) - Method in class net.sf.basedb.core.plugin.AbstractPlugin

Get the value for a job or configuration parameter.

getJobParameterObjectsFromXML(String, boolean) - Method in class net.sf.basedb.plugins.Base1PluginExecuter

getJobParameters() - Method in class net.sf.basedb.plugins.Base1PluginExecuter

Reads the configuration file an creates the parameters found there.

getJobParametersFromXML(String, boolean) - Method in class net.sf.basedb.plugins.Base1PluginExecuter

getJobs() - Method in class net.sf.basedb.core.data.ExperimentData

This is the inverse end.

getJobs() - Method in class net.sf.basedb.core.PluginConfiguration

Get a query that returns the jobs using this plugin configuration.

getJobSessionControl(Job) - Method in class net.sf.basedb.core.SessionControl

Create a new session control for executing a job.

getJobType() - Method in class net.sf.basedb.core.Job

Get the type of job, ie. if it is a job executed by a plugin or not.

getJoinAlias() - Method in class net.sf.basedb.core.ExtraValue

The alias used when joining this extra value into a query.

getJoinAlias() - Method in class net.sf.basedb.core.query.AnnotationExpression

getJoinAlias() - Method in class net.sf.basedb.core.query.ReporterListExpression

getJoinExpression() - Method in enum class net.sf.basedb.core.query.JoinType

getJoinProperty() - Method in class net.sf.basedb.core.query.ReporterListExpression

getJspContext() - Method in class net.sf.basedb.clients.web.extensions.edit.AbstractOnSaveAction

Set the JSP context of the current invokation.

getJspContext() - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerUtil

Get the JSP context.

getJspPage() - Method in class net.sf.basedb.core.RequestInformation

The name of the jsp page to use for displaying the input form for requesting parameters.

getKey() - Method in class net.sf.basedb.util.bfs.MetadataModel.SectionEntry

Get the key of the entry.

getKey() - Method in class net.sf.basedb.util.Enumeration.Entry

getKey() - Method in class net.sf.basedb.util.fuzzy.StringMatcher.FuzzyMatch

Get the key string.

getKey() - Method in class net.sf.basedb.util.StaticCache.LockEntry

getKey(int) - Method in class net.sf.basedb.util.bfs.MetadataModel.Section

Get the key of the entry at the given index.

getKey(int) - Method in class net.sf.basedb.util.Enumeration

getKey(String, Item, Item, SyncFilter.SourceItemTransform, Set<Integer>) - Static method in class net.sf.basedb.util.listable.TransformCache

getKey(Item, Item, SyncFilter.SourceItemTransform, Set<Integer>) - Static method in class net.sf.basedb.util.listable.TransformCache

Get a key that is able to identify a given transformation.

getKeyId() - Method in class net.sf.basedb.core.data.keyring.KeyPermission

Get the id of the key.

getKeyId() - Method in class net.sf.basedb.core.data.keyring.PluginKeys

Gets the id of the RoleKey

getKeys() - Method in class net.sf.basedb.core.data.RoleData

This is the inverse end.

getKeys() - Method in class net.sf.basedb.core.Presets.Preset

Get all keys in this preset.

getKeys() - Method in class net.sf.basedb.util.QueryParameters

Get all keys that are present in the query string.

getKit() - Method in class net.sf.basedb.core.BioMaterialEvent

Get the Kit that was used in this event.

getKit() - Method in class net.sf.basedb.core.BioPlateEvent

Get the Kit that was used in this event.

getKit() - Method in class net.sf.basedb.core.data.BioMaterialEventData

Get the kit used in this event.

getKit() - Method in class net.sf.basedb.core.data.BioPlateEventData

Get the kit used in this event.

getKit() - Method in class net.sf.basedb.core.data.DerivedBioAssayData

Get the kit used to create this bioassay set.

getKit() - Method in class net.sf.basedb.core.DerivedBioAssay

Get the Kit that was used when creating this bioassay.

getLabel() - Method in class net.sf.basedb.core.data.ParameterValueData

Get the label of the parameter.

getLabel() - Method in class net.sf.basedb.core.ParameterInfo

getLabel() - Method in class net.sf.basedb.core.PluginParameter

Get the label of the parameter.

getLastAccess() - Method in class net.sf.basedb.core.SessionControl

Get the time this object last was accessed.

getLastColumn() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo

Get the column number for the last column that contains data.

getLastError() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension

getLastError() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint

getLastExtensionError(String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Get information about the last error that happened when rendering an extension.

getLastExtensionError(String) - Method in class net.sf.basedb.util.extensions.Registry

Get information about the last error that happened when rendering an extension.

getLastExtensionPointError(String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Get information about the last error that happened when rendering an extension point.

getLastExtensionPointError(String) - Method in class net.sf.basedb.util.extensions.Registry

Get information about the last error that happened when rendering an extension point.

getLastGuiContext() - Method in class net.sf.basedb.core.Job

Get the gui-context that was active when this job was created.

getLastModified() - Method in class net.sf.basedb.util.uri.UriMetadata

Get the date and time the resource was last modified.

getLastModified(HttpResponse) - Static method in class net.sf.basedb.util.HttpUtil

Get the date the content was last modified from the headers in the response.

getLastProcessResults() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager

Get the results of the last processing.

getLastRemoteId() - Method in class net.sf.basedb.core.data.UserDeviceData

Get the remote id (=ip address) of the last login from this device.

getLastRemoteId() - Method in class net.sf.basedb.core.UserDevice

Get the remote ID of the host the user used for this device the last time.

getLastRow() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo

Get the row number for the last row that contains data.

getLastScanResults() - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Get the results of the last scan (manual or automatic).

getLastSource() - Method in class net.sf.basedb.core.data.ReporterData

Get the source that was used when this reporter was last updated.

getLastSyncMatchingSource() - Method in class net.sf.basedb.core.SyncFilter

Get the number of source items that matched this particular filter during the last synchronization.

getLastSyncMatchingTransformed() - Method in class net.sf.basedb.core.SyncFilter

Get the number of transformed items that matched this particular filter during the last synchronization.

getLastSyncProperties() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData

A string representation of properties that was affecting that last filter during the last sync.

getLastUpdate() - Method in class net.sf.basedb.core.Annotation

Get the date and time the values in this annotation was last updated.

getLastUpdate() - Method in class net.sf.basedb.core.data.AnnotationData

Get the date and time the values in this annotation was last updated.

getLastUpdate() - Method in class net.sf.basedb.core.data.FileData

Get the date and time the actual file data was last updated.

getLastUpdate() - Method in class net.sf.basedb.core.data.ReporterData

Get the date and time the information about this reporter last was updated.

getLastUpdate() - Method in class net.sf.basedb.core.File

Get the date and time the actual file data was last updated.

getLastUpdated() - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlot

getLastUsed() - Method in class net.sf.basedb.core.data.UserDeviceData

Get the date and time the user last logged in from this device.

getLastUsed() - Method in class net.sf.basedb.core.UserDevice

Get the date and time the user last used this device.

getLatitude() - Method in class net.sf.basedb.util.GeoLocation

getLayerNo() - Method in class net.sf.basedb.core.data.DataCubeLayerData

The layer number of this layer in the data cube.

getLayerNo() - Method in class net.sf.basedb.core.DataCubeLayer

Get the number of this layer.

getLayers() - Method in class net.sf.basedb.core.data.DataCubeData

This is the inverse end.

getLeftTableAlias(Query) - Method in class net.sf.basedb.core.RealJoin

getLeftTableColumn() - Method in class net.sf.basedb.core.RealJoin

getLength() - Method in class net.sf.basedb.core.data.ReporterClonePropertyData

The maximum length of string value types.

getLength() - Method in class net.sf.basedb.core.ExtendedProperty

Get the maximum allowed length of the property value.

getLength() - Method in class net.sf.basedb.core.plugin.ImportInputStream

Get the length of the stream in number of bytes.

getLength() - Method in class net.sf.basedb.util.FileImportInputStream

Calls File.getSize() to get the file size.

getLength() - Method in class net.sf.basedb.util.uri.UriMetadata

Get the length in bytes of the resource.

getLevel() - Method in class net.sf.basedb.util.extensions.logging.LogEntry

The level of the log entry.

getLimit() - Method in class net.sf.basedb.core.signal.ProgressReporterSignalHandler

Get the percentage limit where signal checking becomes disabled.

getLimitHandler() - Method in class net.sf.basedb.core.AbstractSqlQuery

Get a handler for adding LIMIT and OFFSET parameters to an SQL statement.

getLine(int) - Method in class net.sf.basedb.util.parser.FlatFileParser

Get the line with the specified number.

getLineCount() - Method in class net.sf.basedb.util.bfs.MetadataWriter

Get the number of lines that has been written to this file so far, including all comment lines, empty lines, sections headers, etc.

getLineCount() - Method in class net.sf.basedb.util.parser.FlatFileParser

Get the number of lines that the FlatFileParser.parseHeaders() method parsed.

getLines() - Method in class net.sf.basedb.util.parser.FlatFileParser

Get the lines read by FlatFileParser.parseHeaders().

getLink(String, String, Item, int, boolean) - Static method in class net.sf.basedb.clients.web.Base

getLink(String, String, Item, int, boolean, String) - Static method in class net.sf.basedb.clients.web.Base

getLink(String, Nameable, Integer, boolean, boolean, boolean, boolean) - Static method in class net.sf.basedb.clients.web.ChangeHistoryUtil

getLink(S) - Method in class net.sf.basedb.core.AnyToAny.FastLinkLoader

Get the any-to-any link.

getLinkedFile(String, File, boolean, boolean, boolean, String) - Static method in class net.sf.basedb.clients.web.Base

getLinkedItem(DbControl, BasicItem) - Method in class net.sf.basedb.clients.web.plugins.AnyToAnyDataLoader

Get the item that is linked to by this any-to-any link definition.

getLinkedName(String, Nameable, boolean, boolean) - Static method in class net.sf.basedb.clients.web.Base

getLinkName() - Method in class net.sf.basedb.core.AnyToAny.FastLinkLoader

The link name.

getLinkName() - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics

Get the name of the link.

getLinksFrom(BasicItem) - Static method in class net.sf.basedb.core.AnyToAny

Get a query that returns all links linking from the specified item.

getLinksTo(BasicItem) - Static method in class net.sf.basedb.core.AnyToAny

Get a query that returns all links linking to the specified item.

getList() - Method in class net.sf.basedb.clients.web.taglib.table.CellValue

getListableItems() - Static method in class net.sf.basedb.core.Metadata

Get a set containing all Listable item types.

getListableItems(Item, SyncFilter.SourceItemTransform) - Static method in class net.sf.basedb.util.listable.ListableUtil

Get all item types that can have the specified relation to the with the given item type.

getListMemberType() - Method in class net.sf.basedb.core.SyncFilter

getLobHelper() - Method in class net.sf.basedb.core.hibernate.SessionWrapper

getLocale() - Static method in class net.sf.basedb.core.Config

Get the default locale configured for the server.

getLocale() - Method in class net.sf.basedb.core.SessionControl

Get the locale that is curently assigned to this session control.

getLocale() - Method in class net.sf.basedb.util.resources.ResourceBundleWrapper

Get the actual locale used by the bundle, which may be a different locale from the one that was used to load it.

getLocalHost() - Static method in class net.sf.basedb.util.SocketUtil

Get the local address of the local host.

getLocalSignalHandlerId(SignalHandler) - Method in class net.sf.basedb.core.signal.AbstractSignalReceiver

Get the local signal handler id of the given signal handler.

getLocation() - Method in class net.sf.basedb.core.data.DiskUsageData

Get the location of the DiskConsumable item.

getLocation() - Method in class net.sf.basedb.core.data.FileData

Get the Location of this FileData

getLocation() - Method in class net.sf.basedb.core.data.QuotaIndex

getLocation() - Method in class net.sf.basedb.core.data.SessionData

Get the location of the user (if known).

getLocation() - Method in class net.sf.basedb.core.data.UserDeviceData

Get the location of the user (if known).

getLocation() - Method in interface net.sf.basedb.core.DiskConsumable

Get the Location the items is stored at.

getLocation() - Method in class net.sf.basedb.core.DiskUsage

Get the location of the DiskConsumable item.

getLocation() - Method in class net.sf.basedb.core.Experiment

Always Location.PRIMARY.

getLocation() - Method in class net.sf.basedb.core.File

getLocation() - Method in class net.sf.basedb.core.RawBioAssay

Always Location.PRIMARY.

getLocation() - Method in class net.sf.basedb.core.Session

Get the location of the host the user used for this session.

getLocation() - Method in class net.sf.basedb.core.UserDevice

Get the last known location of the device.

getLocation(AuthenticationMethod) - Method in class net.sf.basedb.core.SessionControl

getLocationFromIp(String) - Static method in class net.sf.basedb.util.GeoLocation

Try to convert the given ip address to a location.

getLocationLatitude() - Method in class net.sf.basedb.core.data.SessionData

Get the location latitude of the user (if known).

getLocationLatitude() - Method in class net.sf.basedb.core.data.UserDeviceData

Get the location latitude of the user (if known).

getLocationLatitude() - Method in class net.sf.basedb.core.Session

Get the location latitude of the host the user used for this session.

getLocationLatitude() - Method in class net.sf.basedb.core.UserDevice

Get the last known location latitude of the device.

getLocationLongitude() - Method in class net.sf.basedb.core.data.SessionData

Get the location longitude of the user (if known).

getLocationLongitude() - Method in class net.sf.basedb.core.data.UserDeviceData

Get the location longitude of the user (if known).

getLocationLongitude() - Method in class net.sf.basedb.core.Session

Get the location longitude of the host the user used for this session.

getLocationLongitude() - Method in class net.sf.basedb.core.UserDevice

Get the last known location longitude of the device.

getLockMode() - Method in class net.sf.basedb.core.BioPlateType

Get the lock mode for wells located on plates of this plate type.

getLockMode() - Method in class net.sf.basedb.core.BioWell

Get the lock mode of this well.

getLockMode() - Method in class net.sf.basedb.core.data.BioPlateTypeData

A flag indicating if plates with this type have locked wells or not. 0 = not locked; 1 = locked-after-move; 2 = locked-after-add; 3=locked-after-create

getLockMode() - Method in class net.sf.basedb.core.hibernate.QueryWrapper

getLockMode(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

getLockOptions() - Method in class net.sf.basedb.core.hibernate.QueryWrapper

getLog(String, boolean) - Static method in class net.sf.basedb.util.extensions.logging.ExtensionsLog

Get the service log for the given extension.

getLogChangeType() - Method in enum class net.sf.basedb.core.AnnotationBatcher.Change

getLogControl() - Method in class net.sf.basedb.core.DbControl

Get the log controller for this db control.

getLogControl() - Method in class net.sf.basedb.core.log.db.DbLogManager

getLogControl() - Method in interface net.sf.basedb.core.log.LogManager

Get the log controller that is used in this transaction.

getLogEntries() - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog

Get an iterator that is returning all entries in the log.

getLoggedInUserId() - Method in class net.sf.basedb.core.SessionControl

Get the id of the logged in user, or 0 if no user is logged in.

getLoggedInUserLogin() - Method in class net.sf.basedb.core.SessionControl

Get the login name of the currently logged in user.

getLoggedInUserName() - Method in class net.sf.basedb.core.SessionControl

Get the name of the currently logged in user.

getLogger() - Static method in class net.sf.basedb.core.Application

Get the BASE core logger.

getLogger(String, boolean) - Static method in class net.sf.basedb.util.extensions.logging.ExtensionsLog

Get a logger that can add entries to the log for the given extension.

getLoggingInterceptor() - Method in class net.sf.basedb.core.DbControl

Get the logging interceptor for this db control.

getLogin() - Method in class net.sf.basedb.clients.jobagent.Agent

Get the agent.user configuration value.

getLogin() - Method in class net.sf.basedb.core.authentication.AuthenticatedUser

Get the login string for the user.

getLogin() - Method in class net.sf.basedb.core.authentication.LoginRequest

Get the login name to use.

getLogin() - Method in class net.sf.basedb.core.data.UserData

Get the login for the user account.

getLogin() - Method in class net.sf.basedb.core.User

Get the login for the user account.

getLoginComment() - Method in class net.sf.basedb.core.data.SessionData

Get the login comment.

getLoginComment() - Method in class net.sf.basedb.core.Session

Get the login comment.

getLoginField() - Method in interface net.sf.basedb.clients.web.extensions.login.LoginFormAction

Get attributes for the login field on the form.

getLoginField() - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean

getLoginField() - Method in class net.sf.basedb.clients.web.extensions.login.PasswordLoginFormFactory

getLogInfo() - Method in class net.sf.basedb.core.log.ManualLogEntry

Get information about the log entry.

getLoginRequest() - Method in class net.sf.basedb.core.AuthenticationContext

Get the login request information.

getLoginTime() - Method in class net.sf.basedb.core.data.SessionData

Get the date and time the user logged in.

getLoginTime() - Method in class net.sf.basedb.core.Session

Get the date and time the user logged in.

getLogManager(LogControl) - Method in class net.sf.basedb.core.log.db.DbLogManagerFactory

Creates a new DbLogManager.

getLogManager(LogControl) - Method in interface net.sf.basedb.core.log.LogManagerFactory

Get/create a log manager to log events in a given transaction.

getLogoutTime() - Method in class net.sf.basedb.core.data.SessionData

Get the date and time the user logged out.

getLogoutTime() - Method in class net.sf.basedb.core.Session

Get the date and time the user logged out.

getLong(int, NumberFormat, boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser.Data

Get the value as a long.

getLong(int, NumberFormat, boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser.ExcelData

getLong(String) - Static method in class net.sf.basedb.util.Values

Convert a string to a long.

getLong(String[]) - Static method in class net.sf.basedb.util.Values

Convert an array of strings to an array of Long:s.

getLong(String, long) - Static method in class net.sf.basedb.core.Config

Get the configuration setting specified by key as a long value.

getLong(String, long) - Static method in class net.sf.basedb.util.Values

Convert a string to an long.

getLong(String, Long) - Static method in class net.sf.basedb.util.Values

Convert a string to an long.

getLong(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.ColumnMapper

getLong(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.CompoundMapper

getLong(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.ConstantMapper

getLong(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.CropStringMapper

getLong(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.JepMapper

getLong(FlatFileParser.Data) - Method in interface net.sf.basedb.util.parser.Mapper

Get the value for the line of data as a long.

getLong(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.NullIfExceptionMapper

getLong(HttpResponse, String, Long) - Static method in class net.sf.basedb.util.HttpUtil

getLongFormatter(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory

Get the logged in user's formatter for long numbers.

getLongitude() - Method in class net.sf.basedb.util.GeoLocation

getLongOption(String, Long) - Method in class net.sf.basedb.core.AnnotationType

Get an option and convert the value to a long.

getLongValues() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink

getLowerLimit() - Method in class net.sf.basedb.core.DoubleParameterType

Get the lowst valid value of the parameter.

getLowerLimit() - Method in class net.sf.basedb.core.FloatParameterType

Get the lowst valid value of the parameter.

getLowerLimit() - Method in class net.sf.basedb.core.IntegerParameterType

Get the lowest valid value of the parameter.

getLowerLimit() - Method in class net.sf.basedb.core.LongParameterType

Get the lowest valid value of the parameter.

getMACalculator() - Method in enum class net.sf.basedb.core.IntensityTransform

Get a MA calculator implementation that is suitable for calculating MA-values for the given source data type.

getMainContext(Item) - Method in class net.sf.basedb.clients.web.ModeInfo

Get a main context for this mode.

getMainHqlQuery(DbControl, Class<R>) - Method in class net.sf.basedb.core.AbstractHqlQuery

Build the main query and set parameter values for it.

getMainItemType() - Method in class net.sf.basedb.core.ItemSubtype

Get the main item type that the subtype belongs to.

getMainQuery(DbControl, boolean) - Method in class net.sf.basedb.core.AbstractQuery

Build the main query string.

getMaintenance() - Static method in class net.sf.basedb.core.Version

Get the maintentance version.

getMaintenanceVersion() - Static method in class net.sf.basedb.core.Application

Get the maintenance version.

getMainType() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport

getMainType() - Method in class net.sf.basedb.core.data.PluginDefinitionData

Get the main type of plugin.

getMainType() - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

getMainType() - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin

getMainType() - Method in interface net.sf.basedb.core.plugin.Plugin

Get the type of the plugin.

getMainType() - Method in class net.sf.basedb.core.PluginDefinition

Get the type of plugin.

getMainType() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

Return Plugin.MainType.IMPORT.

getMainType() - Method in class net.sf.basedb.plugins.BfsExporterPlugin

getMainType() - Method in class net.sf.basedb.plugins.CdfFileReporterImporter

getMainType() - Method in class net.sf.basedb.plugins.CloneReportersPlugin

getMainType() - Method in class net.sf.basedb.plugins.executor.BaseFileExporterSupport

getMainType() - Method in class net.sf.basedb.plugins.executor.BaseFileImporterSupport

getMainType() - Method in class net.sf.basedb.plugins.executor.BfsExporterSupport

getMainType() - Method in class net.sf.basedb.plugins.executor.BfsImporterSupport

getMainType() - Method in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport

getMainType() - Method in class net.sf.basedb.plugins.HelpImporter

getMainType() - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin

Returns the main plugin type this plugin belongs to.

getMainType() - Method in class net.sf.basedb.plugins.PluginConfigurationImporter

getMainType() - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker

getMajor() - Static method in class net.sf.basedb.core.Version

Get the major version.

getMajorVersion() - Static method in class net.sf.basedb.core.Application

Get the major version.

getManualConfigureParameters() - Method in class net.sf.basedb.plugins.Base1PluginExecuter

Creates the information needed for manual configuration and initiates the parameters.

getMapper(String) - Method in class net.sf.basedb.util.parser.FlatFileParser

Get a mapper using the default number format.

getMapper(String, boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser

Get a mapper using the default number format.

getMapper(String, NumberFormat) - Method in class net.sf.basedb.util.parser.FlatFileParser

Get a mapper using a specific number format.

getMapper(String, NumberFormat, boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser

getMapper(String, NumberFormat, boolean, JepFunction...) - Method in class net.sf.basedb.util.parser.FlatFileParser

getMapper(String, NumberFormat, Formatter<Date>, boolean, JepFunction...) - Method in class net.sf.basedb.util.parser.FlatFileParser

Create a mapper object that maps an expression string to a value.

getMapper(String, Formatter<Date>, boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser

Get a mapper using the specified date format.

getMapper(String, JepFunction...) - Method in class net.sf.basedb.util.parser.FlatFileParser

getMapper(FlatFileParser, String, Integer, Mapper) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

getMapper(FlatFileParser, String, Integer, Mapper, JepFunction...) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

Get a mapper for the specified flat file parser.

getMapping() - Static method in class net.sf.basedb.core.HibernateUtil

getMappingBatcher() - Method in class net.sf.basedb.core.BioAssaySet

Get a batcher used to insert mappings to raw data.

getMappingBatcher() - Method in class net.sf.basedb.core.DataCube

getMappings() - Method in class net.sf.basedb.core.data.VirtualDbData

The number of cube mappings in the virtual database.

getMappings() - Method in class net.sf.basedb.core.VirtualDb

Get the number of DataCubeMapping:s in this virtual database.

getMasterReporterJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicReporterQuery

Get a joiner instance for joining the master reporter table when the root query is against the cloned reporters table.

getMatching(DbControl) - Method in class net.sf.basedb.core.SyncFilter

getMatchingReporters(DbControl) - Method in class net.sf.basedb.clients.web.ExperimentExplorer

Get the number of reporters matching the current reporter filter.

getMatchingSource() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData

The number of matching source items during that last sync.

getMatchingTransformed() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData

The number of matching items after the transform during that last sync.

getMax() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin

Get the maximum of all values in this bin.

getMaxAge() - Method in class net.sf.basedb.core.DiskUsageStatistics

Get the max age in seconds for a disk usage summary object before it is reloaded from the database again.

getMaxBaseVersion() - Method in interface net.sf.basedb.core.plugin.About

Get the maximum BASE version were to plug-in no longer is expected to work.

getMaxBaseVersion() - Method in class net.sf.basedb.core.plugin.AboutImpl

getMaxBaseVersion() - Method in class net.sf.basedb.util.extensions.AboutBean

getMaxBaseVersion() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout

getMaxBytes() - Method in class net.sf.basedb.core.data.QuotaIndex

getMaxEntries() - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog

Get the max number of entries to keep in the log.

getMaxLength() - Method in class net.sf.basedb.core.AnnotationType

Get the maximum allowed string length for a Type.STRING annotation.

getMaxLength() - Method in class net.sf.basedb.core.StringParameterType

Get the max length of the parameter.

getMaxMemory() - Method in class net.sf.basedb.core.data.JobAgentSettingsData

The max amount of memory the plugin can use.

getMaxMemory() - Method in class net.sf.basedb.core.data.PluginDefinitionData

The max amount of memory the plugin can use.

getMaxMemory() - Method in class net.sf.basedb.core.JobAgentSettings

Get the maximum amount of memory the plugin is allowed to use.

getMaxMemory() - Method in class net.sf.basedb.core.PluginDefinition

Get the maximum amount of memory the plugins is allowed to use.

getMaxParametersInQuery() - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine

Returns 10000.

getMaxParametersInQuery() - Method in interface net.sf.basedb.core.dbengine.DbEngine

Get the maximum number of parameters that can be used in a prepared statement for a query.

getMaxProjectPermission() - Method in class net.sf.basedb.core.Keyring

Get the max project permission within the currently active project.

getMaxRandomSamples() - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics.Options

getMaxRawMappingsForSpot() - Method in class net.sf.basedb.core.BioAssaySet

Get the number of mappings to raw data spots for the spot with the most number of mappings.

getMaxRawMappingsForSpot() - Method in class net.sf.basedb.core.data.DataCubeData

The maximum number of raw data spots a single spot in this data cube is mapped to.

getMaxRawMappingsForSpot() - Method in class net.sf.basedb.core.DataCube

Get the number of mappings to raw data spots for the spot with the most number of mappings.

getMaxRecent(SessionControl) - Static method in class net.sf.basedb.clients.web.Base

Get the setting for the maximum number of recently used items to save.

getMaxResults() - Method in class net.sf.basedb.core.AbstractQuery

getMaxResults() - Method in class net.sf.basedb.core.hibernate.QueryWrapper

getMaxResults() - Method in interface net.sf.basedb.core.query.Query

The maximum number of rows returned by the query.

getMaxUrlLength() - Method in class net.sf.basedb.clients.web.taglib.Page

getMaxValue() - Method in class net.sf.basedb.core.Coloring

Get the value that represents the maximum value.

getMaxValue() - Method in class net.sf.basedb.core.data.ColoringData

The value for the ax endpoint color.

getMaxValueDouble() - Method in class net.sf.basedb.core.AnnotationType

Get the maximum allowed value for a Type.FLOAT or Type.DOUBLE annotation.

getMaxValueLong() - Method in class net.sf.basedb.core.AnnotationType

Get the maximum allowed value for an Type.INT or Type.LONG annotation.

getMaxY(int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramSeries

getMaxY(HistogramPlot.HistogramBin) - Method in enum class net.sf.basedb.util.plot.HistogramPlot.YAggregate

getMaybeGranted() - Method in class net.sf.basedb.core.plugin.Permissions

Get the permissions that the plugin should be granted only if the logged in user already have the permissions.

getMd5() - Method in class net.sf.basedb.core.data.FileData

Get the MD5 hash of the file contents.

getMd5() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData

Get the MD5 hash of the concatenated ID values.

getMd5() - Method in class net.sf.basedb.core.File

Get the MD5 hash of the file contents, or null if not known.

getMd5() - Method in class net.sf.basedb.util.uri.UriMetadata

Get the MD5 checksum of the resource.

getMd5AtLastSync() - Method in class net.sf.basedb.core.data.ItemListData

Get the MD5 hash of the concatenated ID values from the last sync.

getMean() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin

Get the mean of all values in this bin.

getMean(int) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup

Get the mean of the intensity values for the given channel.

getMember() - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext

Get the current file set member information for the file.

getMember() - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter

Always return null.

getMember() - Method in class net.sf.basedb.util.fileset.ValidatingFileSetMember

Get the file set member that this proxy represents.

getMember(DataFileType) - Method in class net.sf.basedb.core.FileSet

Get the member of the given type assuming that there is only a single member of that type.

getMemberRestriction() - Method in class net.sf.basedb.core.ItemList

Get a restriction that mathces members in this list.

getMembers() - Method in class net.sf.basedb.core.data.FileSetData

The members of this file set.

getMembers() - Method in class net.sf.basedb.core.data.ItemListData

Get the set that manages which items that are part of this list.

getMembers() - Method in class net.sf.basedb.core.FileSet

Get the members of this file set.

getMembers() - Method in class net.sf.basedb.core.ItemList

Get a query that returns all items that are members of this list.

getMembers(String) - Method in class net.sf.basedb.core.FileSet

Get a query that returns all members in a file set with a specific generic ItemSubtype.

getMembers(DataFileType) - Method in class net.sf.basedb.core.FileSet

Get a query that returns all members in a file set with a specific DataFileType.

getMemberType() - Method in class net.sf.basedb.core.data.ItemListData

Get the type of items this list can hold.

getMemberType() - Method in class net.sf.basedb.core.ItemList

Get the item type of members on this list.

getMemberTypes() - Method in class net.sf.basedb.core.FileSet

Get a query that return the DataFileType for all members of this file set.

getMenu() - Method in class net.sf.basedb.clients.web.taglib.Page

getMenuId() - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

getMenuId() - Method in interface net.sf.basedb.clients.web.extensions.menu.MenuItemAction

The ID of the menu where this menu item belongs, or null if it belongs to the top-level menu.

getMenuId() - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean

getMessage() - Method in class net.sf.basedb.core.ItemContext

Get a message that should be displayed by a client application as soon as it is appropriate to do so.

getMessage() - Method in class net.sf.basedb.core.PluginResponse

Get the return message from the plugin.

getMessage() - Method in class net.sf.basedb.core.SimpleProgressReporter

Get the last progress message this progress reporter should display.

getMessage() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper

getMessage() - Method in class net.sf.basedb.util.extensions.logging.LogEntry

Get the log message.

getMessage() - Method in class net.sf.basedb.util.fileset.ValidatingFileSetMember

Get the error message if the file failed validation.

getMessage() - Method in class net.sf.basedb.util.overview.Failure

Get a message explaining the failure.

getMessage() - Method in class net.sf.basedb.util.overview.Fix

Get a message explaining what needs to be fixed.

getMessage(String) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper

getMessages() - Method in class net.sf.basedb.core.data.JobData

This is the inverse end.

getMessages() - Method in class net.sf.basedb.core.data.UserData

This is the inverse end.

getMessages() - Method in class net.sf.basedb.core.User

Get a query that returns all messages for the user.

getMessages() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults.FileResults

A list of detailed messages, indicating the results of individual operation on this file.

getMetaColumn() - Method in class net.sf.basedb.core.FeatureCoordinate

getMetadata() - Method in interface net.sf.basedb.util.uri.ConnectionManager

Get metadata about the resource.

getMetadata() - Method in class net.sf.basedb.util.uri.http.HttpConnectionManager

getMetadata(ObjectKey<M>) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile

Get metadata registered for a given given key.

getMetadataKeysOfClass(Class<T>) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile

Get a list of all metadata defined in this extensions file that are keyed with the specified class or interface.

getMetadataParser() - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter

getMetadataPrefix() - Method in class net.sf.basedb.util.basefile.BaseFileWriter

The metadata prefix is written to the beginning of each line that is not a data line.

getMetadataSources() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration

Get an object for registering mapped entity classes.

getMetadataWriter() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter

Get the writer were metadata should be printed.

getMetaGridX() - Method in class net.sf.basedb.core.ArrayDesignBlock

Get the column coordinate of this block.

getMetaGridX() - Method in class net.sf.basedb.core.BlockInfo

Get the row or x meta coordinate.

getMetaGridX() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData

Get the row coordinate of this block.

getMetaGridX() - Method in class net.sf.basedb.core.data.RawData

getMetaGridX() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock

getMetaGridY() - Method in class net.sf.basedb.core.ArrayDesignBlock

Get the row coordinate of this block.

getMetaGridY() - Method in class net.sf.basedb.core.BlockInfo

Get the column or y meta coordinate.

getMetaGridY() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData

Get the column coordinate of this block.

getMetaGridY() - Method in class net.sf.basedb.core.data.RawData

getMetaGridY() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock

getMetamodel() - Method in class net.sf.basedb.core.hibernate.SessionWrapper

getMetaRow() - Method in class net.sf.basedb.core.FeatureCoordinate

getMethod() - Method in class net.sf.basedb.core.authentication.AuthenticationMethod

Get the name of the authentication method.

getMethod() - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter

Always return null.

getMethod() - Method in class net.sf.basedb.plugins.batchimport.AnnotationIdMethod

getMethod() - Method in class net.sf.basedb.plugins.batchimport.FallbackIdMethod

getMethod() - Method in class net.sf.basedb.plugins.batchimport.FileImporter.PathIdMethod

getMethod() - Method in interface net.sf.basedb.plugins.batchimport.IdMethod

The name of this method, which should be unique among the methods that can be used at a given time.

getMethod() - Method in class net.sf.basedb.plugins.batchimport.InternalIdMethod

getMethod() - Method in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod

getMethod() - Method in class net.sf.basedb.plugins.batchimport.PropertyIdMethod

getMethod(Class<?>, String, Class<?>) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory

Get a method with a specific name with optionally, takes a single parameter of given type.

getMethodName() - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter

Always return null.

getMethodName(String, String) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory

Convert the parameter name to a method name.

getMiameAnnotationTypes(DbControl, OverviewContext, Item) - Static method in class net.sf.basedb.util.overview.OverviewUtil

Get all annotation types that has been marked as "Required for MIAME".

getMidValue() - Method in class net.sf.basedb.core.Coloring

Get the value that represents the midpoint value.

getMidValue() - Method in class net.sf.basedb.core.data.ColoringData

The value for the midpoint color.

getMillisecondsSinceStart() - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress

Get the number of milliseconds since the start of the upload.

getMimeType() - Method in class net.sf.basedb.clients.web.fileupload.UploadedFile

Get the MIME type of the uploaded file.

getMimeType() - Method in interface net.sf.basedb.clients.web.plugins.ExportTemplate

Get the MIME type to assign to files generated by this template.

getMimeType() - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate

getMimeType() - Method in class net.sf.basedb.clients.web.plugins.XlsxTemplate

getMimeType() - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate

getMimeType() - Method in class net.sf.basedb.core.data.FileData

Get the mime type of this FileData item.

getMimeType() - Method in class net.sf.basedb.core.File

The mimetype of this File.

getMimeType() - Method in class net.sf.basedb.core.plugin.ImportInputStream

Get the MIME type of the source.

getMimeType() - Method in class net.sf.basedb.util.FileImportInputStream

Calls File.getMimeType().

getMimeType() - Method in class net.sf.basedb.util.uri.UriMetadata

Get the MIME type of the resource.

getMimeType() - Method in class net.sf.basedb.util.zip.Bzip2FilePacker

getMimeType() - Method in interface net.sf.basedb.util.zip.FilePacker

Gets the MIME type to give compressed files from this packer

getMimeType() - Method in class net.sf.basedb.util.zip.GzipFilePacker

getMimeType() - Method in class net.sf.basedb.util.zip.TarFilePacker

getMimeType() - Method in class net.sf.basedb.util.zip.ZipFilePacker

getMimeType(DbControl, String, String) - Static method in class net.sf.basedb.core.MimeType

Get the MIME type of a given file name or extension.

getMimeTypes() - Method in class net.sf.basedb.plugins.Bzip2FileUnpacker

Return a set containing the strings [ application/x-bzip2 ].

getMimeTypes() - Method in class net.sf.basedb.plugins.GzipFileUnpacker

Return a set containing the strings [ application/x-gzip ].

getMimeTypes() - Method in class net.sf.basedb.plugins.TarFileUnpacker

Return a set containing the strings [ application/x-tar, application/x-gzip, application/x-bzip2 ].

getMimeTypes() - Method in class net.sf.basedb.plugins.ZipFileUnpacker

Return a set containing the strings [ application/zip, application/java-archive ].

getMimeTypes() - Method in interface net.sf.basedb.util.zip.FileUnpacker

Get the MIME type for the file formats this unpacker supports.

getMin() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin

Get the minumum of all values in this bin.

getMinBaseVersion() - Method in interface net.sf.basedb.core.plugin.About

Get the minimum BASE version that the plug-in requires.

getMinBaseVersion() - Method in class net.sf.basedb.core.plugin.AboutImpl

getMinBaseVersion() - Method in class net.sf.basedb.util.extensions.AboutBean

getMinBaseVersion() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout

getMinCount() - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics.Options

getMinFraction() - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics.Options

getMinor() - Static method in class net.sf.basedb.core.Version

Get the minor version.

getMinorVersion() - Static method in class net.sf.basedb.core.Application

Get the minor version.

getMinValue() - Method in class net.sf.basedb.core.Coloring

Get the value that represents the minimum value.

getMinValue() - Method in class net.sf.basedb.core.data.ColoringData

The value for the minimum endpoint color.

getMinValueDouble() - Method in class net.sf.basedb.core.AnnotationType

Get the minumum allowed value for a Type.FLOAT or Type.DOUBLE annotation.

getMinValueLong() - Method in class net.sf.basedb.core.AnnotationType

Get the minumum allowed value for an Type.INT or Type.LONG annotation.

getMinY(int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramSeries

getMinY(HistogramPlot.HistogramBin) - Method in enum class net.sf.basedb.util.plot.HistogramPlot.YAggregate

getMissingDataFileTypes() - Method in class net.sf.basedb.core.FileSet

Get a query that is returning all file types that have been marked as required by the associated platform but has no member in this file set.

getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.AnnotationValidator

getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.AnyToAnyValidator

getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.ArrayBatchValidator

The suggested fix is to add an array batch to the slide.

getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.ArrayDesignValidator

The suggested fix is to add an array design to the raw bioassay.

getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.ArraySlideValidator

The suggested fix is to add an array slide to the bioassay.

getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.BasicNodeValidator

Subclasses should override this method if they have a suggessted fix for a missing item problem.

getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.BioPlateValidator

getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.BioSourceValidator

getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.DataFileValidator

getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.DerivedBioAssayValidator

getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.ExperimentalFactorValidator

getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.ExperimentValidator

getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.ExtractValidator

The suggested fix is to add parent extracts to the physical bioassay or one or more extracts to the pooled extract.

getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.FileValidator

getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.HardwareValidator

getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.KitValidator

getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.PhysicalBioAssayValidator

getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.PlatformValidator

getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.ProtocolParameterValidator

getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.ProtocolValidator

getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.RawBioAssayValidator

getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.SampleValidator

The suggested fix is to add a parent sample to the extract or one or more samples to the pooled sample.

getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.SoftwareValidator

getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.TagValidator

getMissingNodeName(Node) - Method in class net.sf.basedb.util.overview.node.AnnotationNameGenerator

getMissingNodeName(Node) - Method in class net.sf.basedb.util.overview.node.AnyToAnyNameGenerator

getMissingNodeName(Node) - Method in class net.sf.basedb.util.overview.node.BioWellNameGenerator

getMissingNodeName(Node) - Method in class net.sf.basedb.util.overview.node.FileSetMemberNameGenerator

getMissingNodeName(Node) - Method in class net.sf.basedb.util.overview.node.ItemListMemberNameGenerator

getMissingNodeName(Node) - Method in class net.sf.basedb.util.overview.node.NameableNameGenerator

getMissingNodeName(Node) - Method in interface net.sf.basedb.util.overview.node.NodeNameGenerator

Generate a name for a node when the item is missing.

getMissingNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.AnnotationNameGenerator

getMissingNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.AnyToAnyNameGenerator

getMissingNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.BioWellNameGenerator

getMissingNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.FileSetMemberNameGenerator

getMissingNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.ItemListMemberNameGenerator

getMissingNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.NameableNameGenerator

getMissingNodeTitle(Node) - Method in interface net.sf.basedb.util.overview.node.NodeNameGenerator

Generate a title for a node when the item is missing.

getModifiedProperties(String, String, String) - Method in class net.sf.basedb.core.log.EntityDetails

Get all modified properties as a string, separating each property name with the given separator.

getMultiPermissions(DbControl, Item, Set<Integer>) - Static method in class net.sf.basedb.util.ShareableUtil

getMultiplicity() - Method in class net.sf.basedb.core.AnnotationType

Get the multiplicity.

getMultiplicity() - Method in class net.sf.basedb.core.data.AnnotationTypeData

How many values are allowed for this annotations of this type. 0 = no limit

getMultiplicity() - Method in class net.sf.basedb.core.ParameterType

Get how many values that can be tied to this parameter. 0 is unlimited values and 1 is default.

getName() - Method in class net.sf.basedb.clients.jobagent.Agent

Get the agent.name configuration value.

getName() - Method in class net.sf.basedb.clients.web.extensions.DynamicActionAttribute

Get the name of the dynamic attribute.

getName() - Method in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory

getName() - Method in interface net.sf.basedb.clients.web.extensions.startpage.StartPageAction

Get the name of the start page.

getName() - Method in class net.sf.basedb.clients.web.extensions.startpage.StartPageBean

getName() - Method in class net.sf.basedb.clients.web.ModeInfo

getName() - Method in class net.sf.basedb.clients.web.SubContext

Get the name of the subcontext.

getName() - Method in class net.sf.basedb.clients.web.taglib.Input

getName() - Method in class net.sf.basedb.clients.web.taglib.table.Hidden

getName() - Method in class net.sf.basedb.core.AnyToAny

getName() - Method in class net.sf.basedb.core.authentication.ExtraUserInformation

The full name of the user.

getName() - Method in class net.sf.basedb.core.BatchedPropertyInfo

Get the name of the property.

getName() - Method in class net.sf.basedb.core.BioAssay

getName() - Method in class net.sf.basedb.core.BioAssaySet

getName() - Method in class net.sf.basedb.core.BioPlateEventType

getName() - Method in class net.sf.basedb.core.BioPlateType

getName() - Method in class net.sf.basedb.core.ChangeHistory

Get the name of the transaction that initiated the change.

getName() - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo

Get the name of the transaction.

getName() - Method in class net.sf.basedb.core.CommonItem

getName() - Method in class net.sf.basedb.core.data.AnyToAnyData

getName() - Method in class net.sf.basedb.core.data.BioAssayData

getName() - Method in class net.sf.basedb.core.data.BioAssaySetData

getName() - Method in class net.sf.basedb.core.data.BioPlateEventTypeData

getName() - Method in class net.sf.basedb.core.data.BioPlateTypeData

getName() - Method in class net.sf.basedb.core.data.ChangeHistoryData

Get the name of the transaction.

getName() - Method in class net.sf.basedb.core.data.ClientDefaultSettingData

Used by Hibernate to link with setting name.

getName() - Method in class net.sf.basedb.core.data.CommonData

getName() - Method in class net.sf.basedb.core.data.ContextData

Get the name of this Context item.

getName() - Method in class net.sf.basedb.core.data.ContextIndex

Get the name of this Context item.

getName() - Method in class net.sf.basedb.core.data.DataFileTypeData

getName() - Method in class net.sf.basedb.core.data.DirectoryData

Get the name of the item.

getName() - Method in class net.sf.basedb.core.data.ExtraValueTypeData

getName() - Method in class net.sf.basedb.core.data.FileData

Get the name of the item.

getName() - Method in class net.sf.basedb.core.data.GlobalDefaultSettingData

Used by Hibernate to link with setting name.

getName() - Method in class net.sf.basedb.core.data.GroupData

getName() - Method in class net.sf.basedb.core.data.HelpData

getName() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData

getName() - Method in class net.sf.basedb.core.data.ItemSubtypeData

Get the name of the subtype which must be unique for subtypes related to a given item type.

getName() - Method in class net.sf.basedb.core.data.MessageData

getName() - Method in class net.sf.basedb.core.data.MimeTypeData

getName() - Method in interface net.sf.basedb.core.data.NameableData

Get the name of the item.

getName() - Method in class net.sf.basedb.core.data.NewsData

getName() - Method in class net.sf.basedb.core.data.PlateEventTypeData

getName() - Method in class net.sf.basedb.core.data.PlateGeometryData

getName() - Method in class net.sf.basedb.core.data.PlatformData

getName() - Method in class net.sf.basedb.core.data.PlatformVariantData

getName() - Method in class net.sf.basedb.core.data.PluginDefinitionData

Get the name of the plugin.

getName() - Method in class net.sf.basedb.core.data.PluginTypeData

getName() - Method in class net.sf.basedb.core.data.ProjectData

getName() - Method in class net.sf.basedb.core.data.QuantityData

getName() - Method in class net.sf.basedb.core.data.QuotaData

getName() - Method in class net.sf.basedb.core.data.QuotaTypeData

getName() - Method in class net.sf.basedb.core.data.ReporterData

getName() - Method in class net.sf.basedb.core.data.ReporterTypeData

getName() - Method in class net.sf.basedb.core.data.RoleData

getName() - Method in class net.sf.basedb.core.data.RoleKeyData

Get the name of the role key.

getName() - Method in class net.sf.basedb.core.data.RootRawBioAssayData

getName() - Method in class net.sf.basedb.core.data.SettingData

Used by Hibernate to link with setting name.

getName() - Method in class net.sf.basedb.core.data.TransformationData

getName() - Method in class net.sf.basedb.core.data.UnitData

getName() - Method in class net.sf.basedb.core.data.UserClientSettingData

Used by Hibernate to link with setting name.

getName() - Method in class net.sf.basedb.core.data.UserData

getName() - Method in class net.sf.basedb.core.data.UserDefaultSettingData

Used by Hibernate to link with setting name.

getName() - Method in class net.sf.basedb.core.data.UserDeviceData

getName() - Method in class net.sf.basedb.core.data.VersionedParameter

Get the parameter name.

getName() - Method in class net.sf.basedb.core.DataFileType

getName() - Method in class net.sf.basedb.core.DbControl

Get the name of this transaction.

getName() - Method in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo

getName() - Method in class net.sf.basedb.core.dbengine.TableInfo.ForeignKeyInfo

getName() - Method in class net.sf.basedb.core.dbengine.TableInfo.IndexInfo

getName() - Method in class net.sf.basedb.core.dbengine.TableInfo.PrimaryKeyInfo

getName() - Method in class net.sf.basedb.core.Directory

getName() - Method in class net.sf.basedb.core.ExtendedProperty

Get the name of the extended property.

getName() - Method in class net.sf.basedb.core.ExtraValueType

getName() - Method in class net.sf.basedb.core.Group

getName() - Method in class net.sf.basedb.core.Help

getName() - Method in class net.sf.basedb.core.IntensityFormula

Get the name of the intensity formula.

getName() - Method in class net.sf.basedb.core.ItemContext

Get the name of this context.

getName() - Method in class net.sf.basedb.core.ItemSubtype

getName() - Method in class net.sf.basedb.core.log.TransactionDetails

Get the name of this transaction.

getName() - Method in class net.sf.basedb.core.LogControl

Get the name of this transaction.

getName() - Method in class net.sf.basedb.core.Message

getName() - Method in class net.sf.basedb.core.MimeType

getName() - Method in interface net.sf.basedb.core.Nameable

Get the name of the item.

getName() - Method in class net.sf.basedb.core.News

getName() - Method in class net.sf.basedb.core.PlateEventType

getName() - Method in class net.sf.basedb.core.PlateGeometry

getName() - Method in class net.sf.basedb.core.Platform

getName() - Method in class net.sf.basedb.core.PlatformVariant

getName() - Method in interface net.sf.basedb.core.plugin.About

The name of the plugin.

getName() - Method in class net.sf.basedb.core.plugin.AboutImpl

getName() - Method in class net.sf.basedb.core.PluginParameter

Get the parameter name.

getName() - Method in class net.sf.basedb.core.PluginType

getName() - Method in class net.sf.basedb.core.Presets.Preset

Get the name of this preset.

getName() - Method in class net.sf.basedb.core.Project

getName() - Method in class net.sf.basedb.core.Quantity

getName() - Method in class net.sf.basedb.core.query.HqlEntityParameterExpression

Get the name of the parameter.

getName() - Method in class net.sf.basedb.core.query.ParameterExpression

Get the name of the parameter.

getName() - Method in class net.sf.basedb.core.query.QueryParameter

Get the name of the parameter.

getName() - Method in class net.sf.basedb.core.Quota

getName() - Method in class net.sf.basedb.core.QuotaType

getName() - Method in class net.sf.basedb.core.RawDataType

Get the name of this raw data type.

getName() - Method in class net.sf.basedb.core.ReporterType

getName() - Method in class net.sf.basedb.core.Role

getName() - Method in class net.sf.basedb.core.RoleKey

getName() - Method in class net.sf.basedb.core.RootRawBioAssay

getName() - Method in class net.sf.basedb.core.Setting

Get the name of this setting.

getName() - Method in class net.sf.basedb.core.signal.Signal

Get the short name of the signal.

getName() - Method in class net.sf.basedb.core.SyncFilter

getName() - Method in class net.sf.basedb.core.Transformation

getName() - Method in class net.sf.basedb.core.Unit

getName() - Method in class net.sf.basedb.core.User

getName() - Method in class net.sf.basedb.core.UserDevice

getName() - Method in class net.sf.basedb.core.VirtualColumn

Get the name of the column.

getName() - Method in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter

getName() - Method in class net.sf.basedb.plugins.executor.ParameterDefinition

Get the name of the parameter.

getName() - Method in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section

getName() - Method in class net.sf.basedb.util.bfs.MetadataModel.Section

Get the name of the section.

getName() - Method in class net.sf.basedb.util.ContextUtil.ContextResult

Get the name of the plug-in configuration or, if the configuration is null, of the plug-in definition

getName() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo

Get the name of the sheet.

getName() - Method in class net.sf.basedb.util.extensions.AboutBean

getName() - Method in interface net.sf.basedb.util.extensions.ExtensionPoint

Get the name of the extension point.

getName() - Method in class net.sf.basedb.util.extensions.ExtensionPointBean

getName() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile

Get the name of the file.

getName() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout

getName() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint

getName() - Method in class net.sf.basedb.util.importer.BaseFileWrapper

getName() - Method in class net.sf.basedb.util.importer.DiskFileWrapper

getName() - Method in interface net.sf.basedb.util.importer.FileWrapper

Get the name of the file.

getName() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay

Get the name of the child bioassay.

getName() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo

Get the name of the file.

getName() - Method in class net.sf.basedb.util.jep.convert.AbsConverter

getName() - Method in class net.sf.basedb.util.jep.convert.AbstractJepConversionFunction

getName() - Method in class net.sf.basedb.util.jep.convert.AddConverter

getName() - Method in class net.sf.basedb.util.jep.convert.AndConverter

getName() - Method in class net.sf.basedb.util.jep.convert.DivideConverter

getName() - Method in class net.sf.basedb.util.jep.convert.EqualsConverter

getName() - Method in class net.sf.basedb.util.jep.convert.ExpConverter

getName() - Method in class net.sf.basedb.util.jep.convert.GreaterConverter

getName() - Method in class net.sf.basedb.util.jep.convert.GreaterEqualsConverter

getName() - Method in class net.sf.basedb.util.jep.convert.IfConverter

getName() - Method in interface net.sf.basedb.util.jep.convert.JepConversionFunction

Get the name of the function or the symbol of the operator

getName() - Method in class net.sf.basedb.util.jep.convert.LessConverter

getName() - Method in class net.sf.basedb.util.jep.convert.LessEqualsConverter

getName() - Method in class net.sf.basedb.util.jep.convert.LogarithmConverter

getName() - Method in class net.sf.basedb.util.jep.convert.MultiplyConverter

getName() - Method in class net.sf.basedb.util.jep.convert.NaturalLogarithmConverter

getName() - Method in class net.sf.basedb.util.jep.convert.NotConverter

getName() - Method in class net.sf.basedb.util.jep.convert.NotEqualsConverter

getName() - Method in class net.sf.basedb.util.jep.convert.OrConverter

getName() - Method in class net.sf.basedb.util.jep.convert.SquareRootConverter

getName() - Method in class net.sf.basedb.util.jep.convert.SubtractConverter

getName() - Method in class net.sf.basedb.util.jep.convert.UMinusConverter

getName() - Method in class net.sf.basedb.util.overview.Node

Get the name of this node.

getName() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramSeries

getName() - Method in class net.sf.basedb.util.plot.PlotAnnotation

The name of the annotation, which will be used as a label in the image.

getName() - Method in class net.sf.basedb.util.resources.ResourceBundleWrapper

Get the base name of the resource bundle.

getName(BasicItem) - Method in class net.sf.basedb.clients.web.taglib.Select

getName(Extension<?>) - Static method in class net.sf.basedb.util.extensions.ExtensionsUtil

Get the name of the extension.

getNameableItems() - Static method in class net.sf.basedb.core.Metadata

Get a set containing all Nameable item types.

getNamedContexts(Item) - Method in class net.sf.basedb.core.SessionControl

Get all named contexts that are owner by the logged in user.

getNamedNativeQuery(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

getNamedNativeQuery(String) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

getNamedParameters() - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

getNamedProcedureCall(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

getNamedProcedureCall(String) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

getNamedQuery(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

If the same query has been executed before, return the cached instance, otherwise create a new query from the parent session and cache it.

getNamedQuery(String) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

If the same query has been executed before, return the cached instance, otherwise create a new query from the parent session and cache it.

getNew(String) - Static method in class net.sf.basedb.core.Reporter

Get a new instance of a reporter, and setting the external ID.

getNew(DbControl) - Static method in class net.sf.basedb.core.AnnotationTypeCategory

Creates a new AnnotationTypeCategory item.

getNew(DbControl) - Static method in class net.sf.basedb.core.BioPlateType

Creates a new bioplate type.

getNew(DbControl) - Static method in class net.sf.basedb.core.BioSource

Create a new BioSource item.

getNew(DbControl) - Static method in class net.sf.basedb.core.Extract

Create a new Extract item.

getNew(DbControl) - Static method in class net.sf.basedb.core.FileServer

Create a new FileServer item.

getNew(DbControl) - Static method in class net.sf.basedb.core.Formula

Create a new Formula item.

getNew(DbControl) - Static method in class net.sf.basedb.core.Group

Create a new Group item.

getNew(DbControl) - Static method in class net.sf.basedb.core.Hardware

Create a new Hardware item.

getNew(DbControl) - Static method in class net.sf.basedb.core.Kit

Create a new Kit item.

getNew(DbControl) - Static method in class net.sf.basedb.core.MimeType

Create a new MimeType item.

getNew(DbControl) - Static method in class net.sf.basedb.core.PermissionTemplate

Create a new permission template item.

getNew(DbControl) - Static method in class net.sf.basedb.core.PhysicalBioAssay

Create a new PhysicalBioAssay item.

getNew(DbControl) - Static method in class net.sf.basedb.core.Project

Create a new Project item.

getNew(DbControl) - Static method in class net.sf.basedb.core.Protocol

Create a new Protocol item.

getNew(DbControl) - Static method in class net.sf.basedb.core.ReporterBatcher

Create a new batcher for reporters.

getNew(DbControl) - Static method in class net.sf.basedb.core.ReporterCloneTemplate

Create a new reporter clone template item.

getNew(DbControl) - Static method in class net.sf.basedb.core.ReporterList

Create a new ReporterList item.

getNew(DbControl) - Static method in class net.sf.basedb.core.ReporterType

Create a new ReporterType item.

getNew(DbControl) - Static method in class net.sf.basedb.core.Role

Create a new Role item.

getNew(DbControl) - Static method in class net.sf.basedb.core.Sample

Create a new Sample item.

getNew(DbControl) - Static method in class net.sf.basedb.core.Software

Create a new Software item.

getNew(DbControl) - Static method in class net.sf.basedb.core.Tag

Create a new Tag item.

getNew(DbControl) - Static method in class net.sf.basedb.core.VirtualDb

Create a new DynamicTables item.

getNew(DbControl, boolean, Job) - Static method in class net.sf.basedb.core.DerivedBioAssay

Create a new parent-less derived bioassay.

getNew(DbControl, int, int) - Static method in class net.sf.basedb.core.PlateGeometry

Create a new PlateGeometry item.

getNew(DbControl, long) - Static method in class net.sf.basedb.core.Quota

Create a new Quota item.

getNew(DbControl, String) - Static method in class net.sf.basedb.core.BioPlateEventType

Creates a new bioplate event type.

getNew(DbControl, String) - Static method in class net.sf.basedb.core.Client

Create a new Client item.

getNew(DbControl, String) - Static method in class net.sf.basedb.core.JobAgent

Create a new JobAgent item.

getNew(DbControl, String) - Static method in class net.sf.basedb.core.Quantity

Create a new Quantity item.

getNew(DbControl, String, int) - Static method in class net.sf.basedb.core.Platform

Create a new file-only platform.

getNew(DbControl, String, String) - Static method in class net.sf.basedb.core.GlobalDefaultSetting

Create a new GlobalDefaultSetting item.

getNew(DbControl, String, String) - Static method in class net.sf.basedb.core.PluginType

Create a new PluginType item.

getNew(DbControl, String, String) - Static method in class net.sf.basedb.core.User

Create a new User item.

getNew(DbControl, String, String, boolean) - Static method in class net.sf.basedb.core.PluginDefinition

Create a new PluginDefinition item.

getNew(DbControl, String, Item) - Static method in class net.sf.basedb.core.DataFileType

Create a new data file type.

getNew(DbControl, String, RawDataType) - Static method in class net.sf.basedb.core.Platform

Create a new platform which may optionally import data into the database.

getNew(DbControl, String, Type) - Static method in class net.sf.basedb.core.ExtraValueType

Create a new ExtraValue item.

getNew(DbControl, Date, Date) - Static method in class net.sf.basedb.core.News

Create a new News item.

getNew(DbControl, Annotatable) - Static method in class net.sf.basedb.core.AnnotationSet

Create a new annotation set for the specified item.

getNew(DbControl, ArrayBatch) - Static method in class net.sf.basedb.core.ArraySlide

Create a new ArraySlide item.

getNew(DbControl, ArrayDesign) - Static method in class net.sf.basedb.core.ArrayBatch

Create a new ArrayBatch item.

getNew(DbControl, ArrayDesign) - Static method in class net.sf.basedb.core.FeatureBatcher

Create a new batcher for regular features.

getNew(DbControl, ArrayDesign, BlockInfo) - Static method in class net.sf.basedb.core.ArrayDesignBlock

getNew(DbControl, BasicItem, BasicItem, String, boolean) - Static method in class net.sf.basedb.core.AnyToAny

Create a new AnyToAny link

getNew(DbControl, BioAssaySet, DataCubeColumn) - Static method in class net.sf.basedb.core.BioAssay

Create a new BioAssay item.

getNew(DbControl, BioAssaySet, ExtraValueType, DataCubeExtraValue, Job) - Static method in class net.sf.basedb.core.ExtraValue

Create a new ExtraValue item.

getNew(DbControl, BioPlateEventParticipant) - Static method in class net.sf.basedb.core.Extract

Create a new Extract item as part of a master bioplate event.

getNew(DbControl, BioPlateEventParticipant) - Static method in class net.sf.basedb.core.PhysicalBioAssay

Create a new PhysicalBioAssay item as part of a master bioplate event.

getNew(DbControl, BioPlateEventParticipant) - Static method in class net.sf.basedb.core.Sample

Create a new Sample item as part of a master bioplate event.

getNew(DbControl, BioPlateEvent, BioPlate) - Static method in class net.sf.basedb.core.BioPlateEventParticipant

Creates a new participant for the given event and bioplate.

getNew(DbControl, BioPlateEventType) - Static method in class net.sf.basedb.core.BioPlateEvent

Create a new BioPlateEvent item.

getNew(DbControl, Client, String) - Static method in class net.sf.basedb.core.Help

Create a new Help item.

getNew(DbControl, Client, String, String) - Static method in class net.sf.basedb.core.ClientDefaultSetting

Create a new ClientDefaultSetting item.

getNew(DbControl, DataCube) - Static method in class net.sf.basedb.core.DataCubeColumn

Create a new DataCubeColumn item.

getNew(DbControl, DataCube) - Static method in class net.sf.basedb.core.DataCubeFilter

Create a new DataCubeFilter item.

getNew(DbControl, DataCube) - Static method in class net.sf.basedb.core.DataCubeLayer

Create a new DataCubeLayer item.

getNew(DbControl, DataCube, Type, ExtraValue.CoordinateType) - Static method in class net.sf.basedb.core.DataCubeExtraValue

Create a new DataCubeExtraValue item.

getNew(DbControl, DerivedBioAssay, Job) - Static method in class net.sf.basedb.core.DerivedBioAssay

Create a new child derived bioassay from a parent derived bioassay.

getNew(DbControl, Directory) - Static method in class net.sf.basedb.core.Directory

Create a new Directory item.

getNew(DbControl, Directory) - Static method in class net.sf.basedb.core.File

Create a new File item.

getNew(DbControl, Experiment, Job) - Static method in class net.sf.basedb.core.Transformation

Create a new Transformation item.

getNew(DbControl, FileSet, File, DataFileType) - Static method in class net.sf.basedb.core.FileSetMember

Create a new member in a file set.

getNew(DbControl, FileStoreEnabled) - Static method in class net.sf.basedb.core.FileSet

Create a new file set for the specified item.

getNew(DbControl, Item) - Static method in class net.sf.basedb.core.ItemList

Create a new ItemList item.

getNew(DbControl, Item) - Static method in class net.sf.basedb.core.ItemSubtype

Create a new item subtype item.

getNew(DbControl, ItemSubtype, DataFileType) - Static method in class net.sf.basedb.core.ItemSubtypeFileType

Create a new item linking a file type to an item subtype.

getNew(DbControl, JobAgent, PluginDefinition) - Static method in class net.sf.basedb.core.JobAgentSettings

Create a new JobAgentSettings item.

getNew(DbControl, MeasuredBioMaterial) - Static method in class net.sf.basedb.core.BioMaterialEvent

Create a new BioMaterialEvent of the BioMaterialEvent.Type.OTHER type.

getNew(DbControl, MeasuredBioMaterial, BioPlateEventParticipant) - Static method in class net.sf.basedb.core.BioMaterialEvent

Create a new BioMaterialEvent of the BioMaterialEvent.Type.OTHER type that is linked with a master BioPlateEventParticipant.

getNew(DbControl, Path) - Static method in class net.sf.basedb.core.Directory

Create a new or existing Directory from a path.

getNew(DbControl, PhysicalBioAssay, Job) - Static method in class net.sf.basedb.core.DerivedBioAssay

Create a new (root) derived bioassay from a physical bioassay.

getNew(DbControl, PlateGeometry) - Static method in class net.sf.basedb.core.PlateType

Create a new PlateType item.

getNew(DbControl, PlateGeometry, int, PlateGeometry, int) - Static method in class net.sf.basedb.core.PlateMapping

Create a new PlateMapping item.

getNew(DbControl, PlateGeometry, BioPlateType) - Static method in class net.sf.basedb.core.BioPlate

Creates a new bioplate with a specific plate geometry and type.

getNew(DbControl, Plate, PlateEventType) - Static method in class net.sf.basedb.core.PlateEvent

Create a new PlateEvent item.

getNew(DbControl, PlateType) - Static method in class net.sf.basedb.core.Plate

Create a new Plate item.

getNew(DbControl, PlateType) - Static method in class net.sf.basedb.core.PlateEventType

Create a new PlateEventType item.

getNew(DbControl, Platform) - Static method in class net.sf.basedb.core.ArrayDesign

Create a new ArrayDesign item for a given platform.

getNew(DbControl, Platform, String) - Static method in class net.sf.basedb.core.PlatformVariant

Create a new variant of a platform.

getNew(DbControl, Platform, String, int) - Static method in class net.sf.basedb.core.PlatformVariant

Create a new file-only variant of a platform.

getNew(DbControl, Platform, String, RawDataType) - Static method in class net.sf.basedb.core.PlatformVariant

Create a new platform variant which may optionally import data into the database.

getNew(DbControl, Platform, PlatformVariant, DataFileType) - Static method in class net.sf.basedb.core.PlatformFileType

Create a new item linking a file type to a platform/variant.

getNew(DbControl, Platform, RawDataType) - Static method in class net.sf.basedb.core.RawBioAssay

Create a new raw bioassay for a specific platform and/or raw data type.

getNew(DbControl, PlatformVariant) - Static method in class net.sf.basedb.core.ArrayDesign

Create a new ArrayDesign item for a given platform variant.

getNew(DbControl, PlatformVariant, RawDataType) - Static method in class net.sf.basedb.core.RawBioAssay

Create a new raw bioassay for a specific platform variant.

getNew(DbControl, PluginDefinition) - Static method in class net.sf.basedb.core.PluginConfiguration

Create a new PluginConfiguration item.

getNew(DbControl, PluginDefinition, PluginConfiguration, Experiment) - Static method in class net.sf.basedb.core.Job

Create a new Job item.

getNew(DbControl, Quantity, String) - Static method in class net.sf.basedb.core.Unit

Create a new Unit item.

getNew(DbControl, RawBioAssay, FeatureIdentificationMethod) - Static method in class net.sf.basedb.core.RawDataBatcher

Create a new batcher for raw data.

getNew(DbControl, RawDataType) - Static method in class net.sf.basedb.core.Experiment

Create a new Experiment item.

getNew(DbControl, Transformation, DataCubeLayer) - Static method in class net.sf.basedb.core.BioAssaySet

Create a new BioAssaySet item.

getNew(DbControl, Type) - Static method in class net.sf.basedb.core.AnnotationType

Create a new AnnotationType item.

getNew(DbControl, User, String, String) - Static method in class net.sf.basedb.core.UserDefaultSetting

Create a new UserDefaultSetting item.

getNew(DbControl, User, String, User, Job) - Static method in class net.sf.basedb.core.Message

Create a new Message item.

getNew(DbControl, User, Client, String, String) - Static method in class net.sf.basedb.core.UserClientSetting

Create a new UserClientSetting item.

getNew(DbControl, VirtualDb) - Static method in class net.sf.basedb.core.DataCube

Create a new DataCube item.

getNewBioAssayEvent(DbControl, PhysicalBioAssay, BioPlateEventParticipant) - Static method in class net.sf.basedb.core.BioMaterialEvent

Create a new BioMaterialEvent of the BioMaterialEvent.Type.BIOASSAY type.

getNewChildren() - Method in class net.sf.basedb.util.overview.Node

Get all new children to this node.

getNewCreationEvent(DbControl, MeasuredBioMaterial, BioPlateEventParticipant) - Static method in class net.sf.basedb.core.BioMaterialEvent

Create a new BioMaterialEvent of the BioMaterialEvent.Type.CREATION type (creation event).

getNewFile(boolean) - Method in class net.sf.basedb.core.File

Get a new random file path.

getNewImageRemapperIfNeeded(ServletContext) - Static method in class net.sf.basedb.clients.web.extensions.skin.ImageRemapperUtil

Get a new image remapper if it is needed, otherwise null.

getNewInherited(DbControl, AnnotationSet, AnnotationData, boolean) - Static method in class net.sf.basedb.core.Annotation

Create a new inherited or cloned annotation.

getNewOrCurrentOverview(DbControl, BasicItem, Project) - Static method in class net.sf.basedb.util.overview.OverviewUtil

Get the current overview or create a new overview.

getNewOrExisting(DbControl, BasicItem, String, BasicItem, boolean) - Static method in class net.sf.basedb.core.AnyToAny

Get a new or existing AnyToAny link.

getNewOrExisting(DbControl, ProjectPermissions) - Static method in class net.sf.basedb.core.ProjectKey

Create a new or load an existing ProjectKey when you have a combination of project/permission values.

getNewOrExisting(DbControl, UserPermissions, GroupPermissions) - Static method in class net.sf.basedb.core.ItemKey

Create a new or load an existing ItemKey when you have a combination of user/group/permission values.

getNewOrExistingId(Session, Map<ProjectData, Integer>) - Static method in class net.sf.basedb.core.ProjectKey

Find the ID of an existing key with exactly the same project/permission combination.

getNewOrExistingKey(Session, Map<UserData, Integer>, Map<GroupData, Integer>) - Static method in class net.sf.basedb.core.ItemKey

Find the ID of an existing key with exactly the same user/group/permission combination.

getNewOverview(DbControl, BasicItem, Project) - Static method in class net.sf.basedb.util.overview.OverviewUtil

Create a new overview for the given item and project.

getNewParameterVersion() - Method in class net.sf.basedb.core.PluginConfiguration

Increase the version number once per transaction.

getNewPrimary(DbControl, AnnotationSet, AnnotationTypeData) - Static method in class net.sf.basedb.core.Annotation

Create a new primary annotation.

getNewsDate() - Method in class net.sf.basedb.core.data.NewsData

Get the news date of this news item.

getNewsDate() - Method in class net.sf.basedb.core.News

Get the date that is shown in listings.

getNewsFeed(String, boolean) - Method in class net.sf.basedb.clients.web.servlet.RssNewsFeed

Generate the XML string for the news feed.

getNewStream() - Method in class net.sf.basedb.util.StreamCacher

Get a new stream that appears to be reading from the start of the master stream.

getNewSystemMessage(DbControl, UserData, String, UserData, JobData) - Static method in class net.sf.basedb.core.Message

Create a new Message from the system.

getNewValue() - Method in class net.sf.basedb.core.ChangeHistory

Get the new value of the property had immediately after this change.

getNewValue() - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData

Get the new value after the change.

getNewValue() - Method in class net.sf.basedb.core.log.ManualLogEntry

New value after the change.

getNewValues() - Method in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo

Get the new annotation values.

getNextColumnId() - Method in class net.sf.basedb.clients.web.taglib.table.ExtensionCells

This is called by the Cell taglib when the next extension column is about to be processed.

getNextColumnNo() - Method in class net.sf.basedb.core.DataCube

Generate the next available column number.

getNextCommand() - Method in class net.sf.basedb.core.PluginResponse

Get the next command sent via Response.Status.CONTINUE.

getNextCubeNo() - Method in class net.sf.basedb.core.VirtualDb

Generate the next available cube number.

getNextEntry(TarInputStream) - Static method in class net.sf.basedb.util.zip.TarUtil

Get the next entry from a TAR input stream.

getNextExtraValueNo() - Method in class net.sf.basedb.core.DataCube

Generate the next available extra value number.

getNextFilename(Object, String) - Method in class net.sf.basedb.util.bfs.SequenceFilenameGenerator

getNextFilename(Object, String) - Method in class net.sf.basedb.util.bfs.SuggestedFilenameGenerator

getNextFilename(T, String) - Method in interface net.sf.basedb.util.bfs.FilenameGenerator

Get the next file name.

getNextFileNumber() - Method in class net.sf.basedb.util.bfs.SequenceFilenameGenerator

Get the next file number.

getNextFilterNo() - Method in class net.sf.basedb.core.DataCube

Generate the next available filter number.

getNextLayerNo() - Method in class net.sf.basedb.core.DataCube

Generate the next available layer number.

getNextLine() - Method in class net.sf.basedb.util.gtf.GtfInputStream

Read the next line from the GTF file and split on tab character.

getNextRequest() - Method in class net.sf.basedb.core.PluginResponse

Get a PluginRequest object that handles the next request, if status is Response.Status.CONTINUE.

getNextRowClass() - Method in class net.sf.basedb.clients.web.taglib.table.Table

getNode() - Method in class net.sf.basedb.core.data.JobData

The name of the node where the job is executing.

getNode() - Method in class net.sf.basedb.core.Job

Get the name of the node where the job is executing.

getNode() - Method in class net.sf.basedb.util.overview.Failure

Get the node that failed validation.

getNode() - Method in class net.sf.basedb.util.Tree.Entry

Get the node element object.

getNode(String) - Method in class net.sf.basedb.util.overview.GenericOverview

Get the node with the given ID.

getNode(K) - Method in class net.sf.basedb.util.overview.cache.NodeCache

getNodeCache() - Method in class net.sf.basedb.util.overview.GenericOverview

This overview implementation doesn't currently support node caching.

getNodeCache() - Method in interface net.sf.basedb.util.overview.OverviewContext

Get the current node cache.

getNodeFactory(DbControl, OverviewContext) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader

Get a node factory that can be used to create item nodes.

getNodeFactory(DbControl, OverviewContext, NodeValidator<? super I>, NodeNameGenerator<? super I>) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader

Get a node factory that can be used to create item nodes using a non-default name generator and validator.

getNodeLoader(OverviewContext, Object) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader

Get a node loader for a specific item type using the current context's node loader factory.

getNodeLoaderFactory() - Method in class net.sf.basedb.util.overview.GenericOverview

Get the current node loader factory.

getNodeLoaderFactory() - Method in interface net.sf.basedb.util.overview.OverviewContext

Get the node loader factory that is used to create node loaders.

getNodeLoaderFactory(OverviewContext) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader

Get the node loader factory used by the current context.

getNodeName(I, Node) - Method in class net.sf.basedb.util.overview.node.NameableNameGenerator

getNodeName(I, Node) - Method in interface net.sf.basedb.util.overview.node.NodeNameGenerator

Generate a name for the new node that is about to be created.

getNodeName(Annotation, Node) - Method in class net.sf.basedb.util.overview.node.AnnotationNameGenerator

getNodeName(AnyToAny, Node) - Method in class net.sf.basedb.util.overview.node.AnyToAnyNameGenerator

getNodeName(FileSetMember, Node) - Method in class net.sf.basedb.util.overview.node.FileSetMemberNameGenerator

getNodeName(Listable, Node) - Method in class net.sf.basedb.util.overview.node.ItemListMemberNameGenerator

getNodeName(MeasuredBioMaterial, Node) - Method in class net.sf.basedb.util.overview.node.BioWellNameGenerator

getNodeNameGenerator() - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader

Get the name generator that is used by this loader.

getNodeTitle(I, Node) - Method in class net.sf.basedb.util.overview.node.NameableNameGenerator

getNodeTitle(I, Node) - Method in interface net.sf.basedb.util.overview.node.NodeNameGenerator

Generate a title for the new node that is about to be created.

getNodeTitle(Annotation, Node) - Method in class net.sf.basedb.util.overview.node.AnnotationNameGenerator

getNodeTitle(AnyToAny, Node) - Method in class net.sf.basedb.util.overview.node.AnyToAnyNameGenerator

getNodeTitle(BioPlate, Node) - Method in class net.sf.basedb.util.overview.node.BioPlateNameGenerator

The base of the title is generated by the superclass.

getNodeTitle(Extract, Node) - Method in class net.sf.basedb.util.overview.node.ExtractNameGenerator

The base of the title is generated by the superclass.

getNodeTitle(FileSetMember, Node) - Method in class net.sf.basedb.util.overview.node.FileSetMemberNameGenerator

getNodeTitle(Listable, Node) - Method in class net.sf.basedb.util.overview.node.ItemListMemberNameGenerator

getNodeTitle(MeasuredBioMaterial, Node) - Method in class net.sf.basedb.util.overview.node.BioWellNameGenerator

getNodeType() - Method in class net.sf.basedb.util.overview.Node

Get the node type of this node.

getNodeValidator() - Method in class net.sf.basedb.util.overview.node.NodeFactory

Get the node validator that is used by this factory.

getNodeValidator(OverviewContext) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader

Get the default node validator for nodes of this type.

getNodeValidatorFactory() - Method in class net.sf.basedb.util.overview.GenericOverview

Get the current node validator factory.

getNodeValidatorFactory() - Method in interface net.sf.basedb.util.overview.OverviewContext

Get the node validator factory that is used to create node validators.

getNodeValidatorFactory(OverviewContext) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader

Get the node validator factory used by the current context.

getNoDuplicates() - Method in class net.sf.basedb.util.annotations.InheritSpecification

getNoSkin() - Method in class net.sf.basedb.clients.web.taglib.Page

getNotNull() - Method in class net.sf.basedb.core.ParameterType

Check if the parameter can be null.

getNulltext() - Method in class net.sf.basedb.clients.web.taglib.PropertyValue

getNullValue() - Method in class net.sf.basedb.util.export.TableWriter

The null value string is written to the output instead of null data values.

getNumAcceptedWithNullReporterOnFeature() - Method in class net.sf.basedb.core.RawDataBatcher

Get the number of accepted inserts because of features with a NULL reporter.

getNumAnnotations() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations

The total numer of annotation values that has been added to this cache.

getNumArrays() - Method in class net.sf.basedb.core.ArrayDesign

Get the number of arrays on a single slide.

getNumArrays() - Method in class net.sf.basedb.core.data.ArrayDesignData

The number of arrays on a single slide.

getNumberFormat() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

Get a number formatter that is able to parse numbers with the specified decimal separator.

getNumberFormat() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil

Get the formatter that is used for formatting cells with numeric values.

getNumberFormat(char, char) - Static method in class net.sf.basedb.util.NumberFormatUtil

getNumberFormatter(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory

Get the logged in user's number formatter for float values.

getNumberOfParameters() - Method in class net.sf.basedb.util.jep.ChannelFunction

getNumberOfParameters() - Method in class net.sf.basedb.util.jep.ExtraValueFunction

getNumberOfParameters() - Method in class net.sf.basedb.util.jep.FunctionSafeJep.UnknownFunction

getNumberOfParameters() - Method in class net.sf.basedb.util.jep.InReporterListFunction

getNumberOfParameters() - Method in class net.sf.basedb.util.jep.LeftFunction

getNumberOfParameters() - Method in class net.sf.basedb.util.jep.Log2Function

getNumberOfParameters() - Method in class net.sf.basedb.util.jep.MeanFunction

getNumberOfParameters() - Method in class net.sf.basedb.util.jep.NotInReporterListFunction

getNumberOfParameters() - Method in class net.sf.basedb.util.jep.PositionFunction

getNumberOfParameters() - Method in class net.sf.basedb.util.jep.RawChannelFunction

getNumberOfParameters() - Method in class net.sf.basedb.util.jep.RawFunction

getNumberOfParameters() - Method in class net.sf.basedb.util.jep.ReporterFunction

getNumberOfParameters() - Method in class net.sf.basedb.util.jep.ScoreFunction

getNumberOfParameters() - Method in class net.sf.basedb.util.jep.SimpleJepFunction

getNumberOfParameters() - Method in class net.sf.basedb.util.parser.ColFunction

getNumberOfParameters() - Method in class net.sf.basedb.util.parser.DataNoFunction

getNumberOfParameters() - Method in class net.sf.basedb.util.parser.DefaultItemFunction

getNumberOfParameters() - Method in class net.sf.basedb.util.parser.LineNoFunction

getNumBioAssays() - Method in class net.sf.basedb.clients.web.ExperimentExplorer

Get the number of bioassays in the bioassayset.

getNumBytes(FlatFileParser) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

Get the number of bytes read from the file.

getNumBytes(FlatFileParser) - Method in class net.sf.basedb.plugins.gtf.GtfReporterImporter

Get the number of bytes read from the original file.

getNumBytes(FlatFileParser) - Method in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter

Get the number of bytes read from the original file.

getNumChildren() - Method in class net.sf.basedb.util.Tree.Entry

Get the number of children added to this node.

getNumColumns() - Method in class net.sf.basedb.core.data.DataCubeData

The number of columns in this data cube.

getNumColumns() - Method in class net.sf.basedb.core.DataCube

Get the number of columns created in this data cube.

getNumDbFeatures() - Method in class net.sf.basedb.core.ArrayDesign

Get the number of features on this array design that are stored in the database.

getNumDbFeatures() - Method in class net.sf.basedb.core.data.ArrayDesignData

The number of features on this array design that are stored in the database.

getNumDbSpots() - Method in class net.sf.basedb.core.RawBioAssay

Get the number of spots on this raw bioassay that are stored in the database.

getNumDecimals(Number) - Method in class net.sf.basedb.util.formatter.AdaptiveNumberFormatter

getNumDecimals(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterSettings

Get the number of decimals a number formatter should display.

getNumDeleted() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager

Get the number of deleted files that was found in the last call to ExtensionsManager.scanForChanges().

getNumDeleted() - Method in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor

Get the total number of resources that was deleted.

getNumEntries() - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog

Get the current number of entries in the log.

getNumError() - Method in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor

Get the number of files that was had an error.

getNumError() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations

Number of annotations that was couldn't be set by the call to the AnnotationFlatFileImporter.NewAnnotations.setNewAnnotations(AnnotationFlatFileImporter, AnnotationBatcher, boolean, boolean, boolean, boolean) method because of an error (too many values).

getNumError() - Method in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor

Get the number of files that was had an error.

getNumError() - Method in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor

Get the number of files that was had an error.

getNumError() - Method in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor

Get the number of files that was had an error.

getNumError() - Method in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor

Get the number of files that was had an error.

getNumError() - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor

Get the number of files that was had an error.

getNumError() - Method in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor

Get the number of files that was had an error.

getNumErrorFiles() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults

The number of extension files that could not be completely loaded because of an error.

getNumErrors() - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog

Get the current number of error entries in the log.

getNumErrors() - Method in class net.sf.basedb.util.overview.Node

Get the number of errors on this node.

getNumExtensions() - Method in class net.sf.basedb.util.extensions.ExtensionsInvoker

Get the number of enabled extensions in this invokation.

getNumExtracted() - Method in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor

Get the total number of resources that was extracts.

getNumExtraValues() - Method in class net.sf.basedb.core.data.DataCubeData

The number of extra values in this data cube.

getNumExtraValues() - Method in class net.sf.basedb.core.DataCube

Get the number of extra values created for this data cube.

getNumFileFeatures() - Method in class net.sf.basedb.core.ArrayDesign

Get the number of features on this array design that are stored inside files.

getNumFileFeatures() - Method in class net.sf.basedb.core.data.ArrayDesignData

The number of features on this array design that are stored inside files.

getNumFileReporters() - Method in class net.sf.basedb.core.BioAssaySet

Get the number of unique reporters for data that is stored in files.

getNumFileReporters() - Method in class net.sf.basedb.core.data.BioAssaySetData

The number of unique reporters as stored in files in this bioassayset.

getNumFiles() - Method in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor

Get the number of files that was successfully processed.

getNumFiles() - Method in class net.sf.basedb.clients.web.extensions.UninstalledFileProcessor

Get the number of files that was processed.

getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor

Get the number of files that was successfully processed.

getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor

Get the number of files that was successfully processed.

getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor

Get the number of files that was successfully processed.

getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.IgnoreFileProcessor

Get the number of files that was processed.

getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.MarkAsProcessedProcessor

Get the number of files that was processed.

getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor

Get the number of files that was successfully processed.

getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor

Get the number of files that was successfully processed.

getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor

Get the number of files that was processed.

getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor

Get the number of files that was successfully processed.

getNumFileSpots() - Method in class net.sf.basedb.core.BioAssay

Get the number of spots that are stored in files.

getNumFileSpots() - Method in class net.sf.basedb.core.BioAssaySet

Get the number of spots that are stored in files.

getNumFileSpots() - Method in class net.sf.basedb.core.data.BioAssayData

The number of unique spots in this bioassayset.

getNumFileSpots() - Method in class net.sf.basedb.core.data.BioAssaySetData

The number of unique spots in this bioassayset.

getNumFileSpots() - Method in class net.sf.basedb.core.data.RawBioAssayData

The number of spots on this raw bioassay that are stored inside files.

getNumFileSpots() - Method in class net.sf.basedb.core.RawBioAssay

Get the number of spots on this raw bioassay that are stored inside files.

getNumFileValues() - Method in class net.sf.basedb.core.data.ExtraValueData

The number of extra values that are stored in files.

getNumFileValues() - Method in class net.sf.basedb.core.ExtraValue

Get the number of values that are stored in files.

getNumFilteredColumns() - Method in class net.sf.basedb.clients.web.taglib.table.Table

getNumFilters() - Method in class net.sf.basedb.core.data.DataCubeData

The number of filters in this data cube.

getNumFilters() - Method in class net.sf.basedb.core.DataCube

Get the number of filters created for this data cube.

getNumFormulas() - Method in class net.sf.basedb.core.Formula

Get the number of expression defined by this formula.

getNumIgnored() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager

Get the number of ignored files that was found in the last call to ExtensionsManager.scanForChanges().

getNumLayers() - Method in class net.sf.basedb.core.data.DataCubeData

The number of layers in this data cube.

getNumLayers() - Method in class net.sf.basedb.core.DataCube

Get the number of layers created in this data cube.

getNumLines() - Method in class net.sf.basedb.util.gtf.GtfInputStream

Get the number of lines parsed so far.

getNumMembers(DataFileType) - Method in class net.sf.basedb.core.FileSet

Get the number of members in the file set of the specified type.

getNumModified() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager

Get the number of modified files that was found in the last call to ExtensionsManager.scanForChanges().

getNumNew() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager

Get the number of new files that was found in the last call to ExtensionsManager.scanForChanges().

getNumPlates() - Method in class net.sf.basedb.core.ArrayDesign

The number of plates connected to this array design.

getNumPlugins() - Method in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor

Get the total number of plug-in installed or updated by the processor.

getNumPlugins() - Method in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor

Get the total number of plug-in installed or updated by the processor.

getNumPositions() - Method in class net.sf.basedb.core.data.DataCubeData

The number of positions in this data cube.

getNumPositions() - Method in class net.sf.basedb.core.DataCube

Get the number of positions created in this data cube.

getNumPositions(DbControl, int) - Method in class net.sf.basedb.clients.web.ExperimentExplorer

Get the number of unique positions the reporter of the specifed index is present in among all the bioassays in the bioassay set.

getNumPropertyFilters() - Method in class net.sf.basedb.core.ItemContext

Get the total number of property filters stored in this context.

getNumPropertyFilters(int) - Method in class net.sf.basedb.core.ItemContext

Get the number of property filters stored in this context for the given filter row.

getNumRead() - Method in class net.sf.basedb.util.InputStreamSplitter

Get the number of bytes that has been read or skipped from the input stream.

getNumRead() - Method in class net.sf.basedb.util.InputStreamTracker

Get the number of bytes read or skipped from the input stream.

getNumRecent(String) - Method in class net.sf.basedb.core.ItemContext

Get the number of recently used value in the list.

getNumRecent(Item) - Method in class net.sf.basedb.core.ItemContext

Get the number of recently used items in the list.

getNumRecent(Item, String) - Method in class net.sf.basedb.core.ItemContext

Get the number of recently used items in a list with a sublist.

getNumRecent(Item, ItemSubtype) - Method in class net.sf.basedb.core.ItemContext

Get the number of recently used items in the list.

getNumRegistered() - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor

Get the number of extensions + extension points that was registered.

getNumRemoved() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations

Number of annotations that was removed by the call to the AnnotationFlatFileImporter.NewAnnotations.setNewAnnotations(AnnotationFlatFileImporter, AnnotationBatcher, boolean, boolean, boolean, boolean) method.

getNumReplaced() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations

Number of annotations that was replaced by the call to the AnnotationFlatFileImporter.NewAnnotations.setNewAnnotations(AnnotationFlatFileImporter, AnnotationBatcher, boolean, boolean, boolean, boolean) method.

getNumReporters() - Method in class net.sf.basedb.clients.web.ExperimentExplorer

Get the total number of unique reporters found in the bioassayset.

getNumReporters() - Method in class net.sf.basedb.core.BioAssaySet

Get the number of unique reporters among all bioassays in this bioassayset.

getNumReporters() - Method in class net.sf.basedb.core.data.BioAssaySetData

The number of unique reporters in this bioassayset.

getNumReportersNotFound() - Method in class net.sf.basedb.core.RawDataBatcher

Get the number of reporters that was not found.

getNumServlets() - Method in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor

Get the total number of servlets found during the last processing.

getNumSet() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations

Number of annotations that was set (=added or replaced) by the call to the AnnotationFlatFileImporter.NewAnnotations.setNewAnnotations(AnnotationFlatFileImporter, AnnotationBatcher, boolean, boolean, boolean, boolean) method.

getNumSheets() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil

Get the number of sheets in the workbook.

getNumSkippedLines() - Method in class net.sf.basedb.util.parser.FlatFileParser

Get the number of lines that the last call to FlatFileParser.nextData() or FlatFileParser.hasMoreData() ignored because they matched the ignore regular expression or couldn't be interpreted as data lines.

getNumSkippedMissingFeature() - Method in class net.sf.basedb.core.RawDataBatcher

Get the number of skipped inserts because of a missing feature.

getNumSpots() - Method in class net.sf.basedb.clients.web.ExperimentExplorer

Get the total number of spots in the bioassayset.

getNumSpots() - Method in class net.sf.basedb.core.BioAssay

Get the number of spots in this bioassay.

getNumSpots() - Method in class net.sf.basedb.core.BioAssaySet

Get the number of spots in all bioassays in this bioassayset.

getNumSpots() - Method in class net.sf.basedb.core.data.BioAssayData

The number of unique spots in this bioassay.

getNumSpots() - Method in class net.sf.basedb.core.data.BioAssaySetData

The number of unique spots in this bioassayset.

getNumStatements() - Method in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget

getNumUniqueTranscriptIds() - Method in class net.sf.basedb.util.gtf.GtfInputStream

Get the number of unique transcript ids found so far.

getNumUnmodified() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager

Get the number of unmodified files that was found in the last call to ExtensionsManager.scanForChanges().

getNumUnregistered() - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor

Get the number of extensions + extension points that was unregistered.

getNumUnregistered() - Method in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor

Get the number of extensions + extension points that was unregistered.

getNumValues() - Method in class net.sf.basedb.core.data.ExtraValueData

The number of extra values that have been inserted.

getNumValues() - Method in class net.sf.basedb.core.ExtraValue

Get the number of extra values inserted.

getNumValues(String) - Method in class net.sf.basedb.util.QueryParameters

Get the number of values for a key.

getNumWarnings() - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog

Get the current number of warning entries in the log.

getNumWarnings() - Method in class net.sf.basedb.util.overview.Node

Get the number of warnings on this node.

getObject(int) - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult

getObject(int) - Method in class net.sf.basedb.core.DynamicResultIterator.SqlResultImpl

getObject(int) - Method in interface net.sf.basedb.core.query.SqlResult

Get the value of the specified column as an object.

getObject(String) - Method in class net.sf.basedb.core.ItemContext

Get an object.

getObjectForKey(ObjectKey<O>) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Get the object that was registered for the given key.

getObjectForKey(ObjectKey<O>) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile

Get the object that was registered for the given key.

getObjectsOfClass(Class<T>) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile

Get a list of all objects defined in this extensions file that are of the specified class or interface.

getOldItem(SessionControl, T, int) - Static method in class net.sf.basedb.clients.web.Base

Get the old item that is stored in the SessionControl:s session setting itemType.item.

getOldValue() - Method in class net.sf.basedb.core.ChangeHistory

Get the old value of the property had before this change.

getOldValue() - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData

Get the previous value before the change.

getOldValue() - Method in class net.sf.basedb.core.log.ManualLogEntry

Old value before the change.

getOldValues() - Method in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo

Get the old annotation values.

getOldValues() - Method in class net.sf.basedb.core.data.ParameterValueData

Get the old values that has been replaced by new values in this session.

getOpen() - Method in class net.sf.basedb.clients.web.taglib.menu.Menu

getOperator() - Method in class net.sf.basedb.core.data.PropertyFilterData

Get the operator used for this filter.

getOperator() - Method in class net.sf.basedb.core.PropertyFilter

Get the operator to use in the filter.

getOperators() - Static method in class net.sf.basedb.util.jep.Jep

Get a list of built-in operators supported by the Jep.jepToExpression(JEP) and Jep.jepToRestriction(JEP) converter.

getOptimizeTableSql(String, String, String) - Method in interface net.sf.basedb.core.dbengine.DbEngine

Generate SQL to optimize a table.

getOptimizeTableSql(String, String, String) - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine

Return null.

getOptimizeTableSql(String, String, String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine

Generate optimize table <catalog>.<table>.

getOptimizeTableSql(String, String, String) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine

Generate VACUUM FULL <schema>.<table>.

getOption(String) - Method in class net.sf.basedb.clients.jobagent.CmdLine

Get the value for the specified option

getOption(String) - Method in class net.sf.basedb.core.AnnotationType

Get an option.

getOption(String) - Method in class net.sf.basedb.plugins.executor.ParameterDefinition

Get the value for an option.

getOption(String, String) - Method in class net.sf.basedb.clients.jobagent.CmdLine

Get the value for an option.

getOption(ValidationRuleAction, String, String) - Method in class net.sf.basedb.util.overview.ValidationOptions

Get the configured option for a validator rule.

getOptionalFilter(Item) - Static method in class net.sf.basedb.core.QueryRuntimeFilterFactory

Get the default optional runtime filter for the speicified item type.

getOptions() - Method in class net.sf.basedb.core.data.AnnotationTypeData

Additional options depending on the value type.

getOptions() - Method in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter

getOptions() - Method in class net.sf.basedb.plugins.executor.ParameterDefinition

Get the names of other options that are defined for this parmeter.

getOrCreate(JspContext, FileViewerContext) - Static method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerUtil

Get an existing instance or create a new instance.

getOrdinal() - Method in class net.sf.basedb.core.data.PlateEventTypeData

The ordinal of this event type among all event types defined for the plate type.

getOrdinal() - Method in class net.sf.basedb.core.PlateEventType

Get the order of this event among the list of events.

getOrganisation() - Method in class net.sf.basedb.core.authentication.ExtraUserInformation

The organisation of the user.

getOrganisation() - Method in class net.sf.basedb.core.data.UserData

Get the organisation this user works for, or null if unknown.

getOrganisation() - Method in class net.sf.basedb.core.User

Get the organisation this user works for, or null if unknown.

getOriginalBioMaterial() - Method in class net.sf.basedb.core.BioWell

Get the original biomaterial that was placed in this biowell.

getOriginalBioMaterial() - Method in class net.sf.basedb.core.data.BioWellData

The MeasuredBioMaterialData used in this well.

getOriginalPermissions() - Method in class net.sf.basedb.core.GroupPermissions

Get the internal representation of the original permissions.

getOriginalPermissions() - Method in class net.sf.basedb.core.ProjectPermissions

Get the internal representation of the original permissions.

getOriginalPermissions() - Method in class net.sf.basedb.core.UserPermissions

Get the internal representation of the original permissions.

getOriginalPermissions(Group) - Method in class net.sf.basedb.core.GroupPermissions

Get the original permissions for a group if this object was created with the GroupPermissions(ItemKey) constructor.

getOriginalPermissions(Project) - Method in class net.sf.basedb.core.ProjectPermissions

Get the original permissions for a project if this object was created with the ProjectPermissions(ProjectKey) constructor.

getOriginalPermissions(User) - Method in class net.sf.basedb.core.UserPermissions

Get the original permissions for a user if this object was created with the UserPermissions(ItemKey) constructor.

getOriginalQuantity() - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData

Get the original quantity of the biomaterial.

getOriginalQuantity() - Method in class net.sf.basedb.core.MeasuredBioMaterial

Get the original quantity of the biomaterial.

getOriginX() - Method in class net.sf.basedb.core.ArrayDesignBlock

Get the distance from the left edge of the slide to the top left spot in the block.

getOriginX() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData

Get the distance from the left edge of the slide to the top left spot in the block.

getOriginX() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock

getOriginY() - Method in class net.sf.basedb.core.ArrayDesignBlock

Get the distance from the top edge of the slide to the top left spot in the block.

getOriginY() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData

Get the distance from the top edge of the slide to the top left spot in the block.

getOriginY() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock

getOut() - Method in class net.sf.basedb.clients.web.extensions.JspContext

Get a writer object that can be used to return generated text to the response that is sent back to the browser.

getOutputStream(File) - Method in class net.sf.basedb.core.Migration

Get a stream for writing to the given file.

getOutputStream(File) - Static method in class net.sf.basedb.util.FileUtil

Get a buffered OutputStream object writing to the specified file.

getOutputStream(String) - Method in class net.sf.basedb.util.bfs.AbstractDataWriterFactory

Create an output stream for writing to a file with the given filename.

getOutputStream(String) - Method in class net.sf.basedb.util.bfs.GenericBaseDataWriterFactory

Create a new file in the data directory with the given file name.

getOutputStream(String) - Method in class net.sf.basedb.util.bfs.GenericDiskDataWriterFactory

Create a new file in the data directory with the given file name.

getOutputStream(String, int) - Method in class net.sf.basedb.util.StaticCache

Get a lock-safe output stream.

getOverrideId() - Method in class net.sf.basedb.core.data.AnnotationData

The ID of the default annotation that this project-specific annotation is overriding. 0 for default annotations.

getOverrideId() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink

getOverrideId() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

Get the id of the default annotation that this project-specific annotation is overriding.

getOverwrite() - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin

Get the configured value for the overwrite parameter.

getOverwrite() - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker

If existing file should be overwritten or not.

getOverwriteAnnotationsParameters(String, String, Boolean) - Method in class net.sf.basedb.core.plugin.AbstractPlugin

Parameter definition that asks if copied annotations should overwrite existing annotations or not.

getOverwriteParameter(String, String) - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin

Get a plugin parameter that asks if existing files can be overwritten or not.

getOverwriteParameter(String, String) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker

Get a plugin parameter that asks if existing files should be overwritten or not.

getOwnableItems() - Static method in class net.sf.basedb.core.Metadata

Get a set containing all Ownable item types.

getOwner() - Method in interface net.sf.basedb.core.data.OwnableData

Get the UserData that is the owner of the item.

getOwner() - Method in class net.sf.basedb.core.data.OwnedData

getOwner() - Method in interface net.sf.basedb.core.Ownable

Get the User that is the owner of the item.

getOwner() - Method in class net.sf.basedb.core.OwnedItem

getPacker() - Method in class net.sf.basedb.plugins.PackedFileExporter

Get the FilePacker that has been configured in the current configuration.

getPacker(String) - Method in class net.sf.basedb.plugins.PackedFileExporter

Create a FilePacker from the given class.

getPage() - Method in class net.sf.basedb.clients.web.taglib.table.Navigator

getPage() - Method in class net.sf.basedb.clients.web.taglib.table.Table

getPage() - Method in class net.sf.basedb.core.data.ContextData

Get the current page number, starting at 0.

getPage() - Method in class net.sf.basedb.core.ItemContext

Get the current table page.

getPageContext() - Method in class net.sf.basedb.clients.web.extensions.JspContext

Get the JSP Page context object for the current request.

getPageType() - Method in class net.sf.basedb.clients.web.ModeInfo

getPageType() - Method in exception net.sf.basedb.clients.web.WebException

Get the page type to display the error message in.

getParameter(int) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

getParameter(int, Class<T>) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

getParameter(String) - Method in class net.sf.basedb.clients.web.extensions.AbstractJspFactory

Get a generic parameter value.

getParameter(String) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload

Get the value for a form field.

getParameter(String) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

getParameter(String) - Method in class net.sf.basedb.core.RequestInformation

Get the plugin parameter with the specified name.

getParameter(String) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter

Get the current value of a 'settings' parameter.

getParameter(String) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter

Get the current value of a parameter.

getParameter(String, Class<T>) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

getParameterClass() - Method in class net.sf.basedb.core.ParameterType

Get the class a value must have to match this parameter type.

getParameterDefinition() - Method in class net.sf.basedb.plugins.executor.ProgramParameter

Get the definition of this parameter.

getParameterDefinitions(boolean) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

Get the current program parameter definitions.

getParameterInfo(String) - Method in class net.sf.basedb.core.Job

Get extra information about a parameter.

getParameterInfo(String) - Method in class net.sf.basedb.core.PluginConfiguration

Get extra information about a parameter in the latest version.

getParameterInfo(String, int) - Method in class net.sf.basedb.core.PluginConfiguration

Get extra information about a parameter in a specific version.

getParameterMetadata() - Method in class net.sf.basedb.core.hibernate.QueryWrapper

getParameterName(String) - Method in class net.sf.basedb.util.extensions.debug.ProxyActionFactory

Convert a method name to a parameter name.

getParameterNames() - Method in class net.sf.basedb.clients.web.fileupload.FileUpload

Get the names for all fields used in the form, excluding file input fields.

getParameterNames() - Method in class net.sf.basedb.core.AbstractQuery

getParameterNames() - Method in class net.sf.basedb.core.Job

Get the names of all parameters for the job.

getParameterNames() - Method in class net.sf.basedb.core.PluginConfiguration

Get the names of all configuration values in the latest version.

getParameterNames() - Method in interface net.sf.basedb.core.query.Query

Get a set with the names for all parameters in this query.

getParameterNames(int) - Method in class net.sf.basedb.core.PluginConfiguration

Get the names of all configuration values in a specific version.

getParameters() - Method in class net.sf.basedb.core.AbstractQuery

Get all query parameters.

getParameters() - Method in class net.sf.basedb.core.data.JobData

The parameters for this job.

getParameters() - Method in class net.sf.basedb.core.data.ProtocolData

This set manages the parameters for this protcol.

getParameters() - Method in class net.sf.basedb.core.hibernate.QueryWrapper

getParameters() - Method in class net.sf.basedb.core.Protocol

Get a query that returns all annotation types used as parameters for this protocol.

getParameters() - Method in class net.sf.basedb.core.RequestInformation

Get a list containing the information about the parameters needed for the current request.

getParametersFromBaseFile(File) - Method in class net.sf.basedb.plugins.Base1PluginExecuter

Get the data from the configuration file.

getParameterType() - Method in class net.sf.basedb.core.PluginParameter

Get the parameter type, which tells the client application the data type and allowed values for the parameter.

getParameterType(Class<T>, List<?>) - Method in class net.sf.basedb.core.PluginConfiguration

Gets the ParameterType to use with a class.

getParameterType(String) - Method in class net.sf.basedb.core.AbstractQuery

Get the type of the parameter, or null if not known.

getParameterValue(int) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

getParameterValue(String) - Method in class net.sf.basedb.core.AbstractQuery

Get the value of the named parameter.

getParameterValue(String) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

getParameterValue(String) - Method in class net.sf.basedb.core.Job

Get the value of a named parameter.

getParameterValue(String) - Method in class net.sf.basedb.core.plugin.NamespaceRequestWrapper

getParameterValue(String) - Method in interface net.sf.basedb.core.plugin.Request

Get the value for the parameter with the specified name.

getParameterValue(String) - Method in class net.sf.basedb.core.PluginRequest.RequestImpl

getParameterValue(String) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper

getParameterValue(String, Class<?>) - Method in class net.sf.basedb.util.extensions.debug.ProxyActionFactory

Get the value of a parameter.

getParameterValue(Parameter<T>) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

getParameterValues() - Method in class net.sf.basedb.core.Job

Get the configuration parameters as a ParameterValues object.

getParameterValues(int) - Method in class net.sf.basedb.core.PluginConfiguration

Get the configuration parameters as a ParameterValues object.

getParameterValues(String) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload

Get an array of values for a form field.

getParameterValues(String) - Method in class net.sf.basedb.core.Job

Get the values of a named parameter.

getParameterValues(String) - Method in class net.sf.basedb.core.plugin.NamespaceRequestWrapper

getParameterValues(String) - Method in interface net.sf.basedb.core.plugin.Request

Get the values for the parameter with the specified name.

getParameterValues(String) - Method in class net.sf.basedb.core.PluginConfiguration

Get the values of a configuration parameter in the latest version.

getParameterValues(String) - Method in class net.sf.basedb.core.PluginRequest.RequestImpl

getParameterValues(String) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper

getParameterValues(String, int) - Method in class net.sf.basedb.core.PluginConfiguration

Get the values of a configuration parameter in a specific version.

getParameterValuesImpl() - Method in class net.sf.basedb.core.Job

Get a write-protected ParameterValuesImpl object.

getParameterValuesImpl(int) - Method in class net.sf.basedb.core.PluginConfiguration

Get a write-protected ParameterValuesImpl object so a job can read the paremeters.

getParameterVersion() - Method in class net.sf.basedb.core.data.JobData

Get the parameter version of the configuration used for this job.

getParameterVersion() - Method in class net.sf.basedb.core.data.PluginConfigurationData

Get the current/latest parameter version.

getParameterVersion() - Method in class net.sf.basedb.core.Job

Get the version number of the configuration parameters used for this job.

getParameterVersion() - Method in class net.sf.basedb.core.PluginConfiguration

Get the latest version number of the parameters.

getParent() - Method in class net.sf.basedb.clients.web.extensions.renderer.PrefixSuffixRenderer

getParent() - Method in class net.sf.basedb.core.data.DirectoryData

Get the parent directory of this directory.

getParent() - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData

Get the parent biomaterial.

getParent() - Method in class net.sf.basedb.core.data.WellData

If the plate was created from a PlateMappingData this property points to the well on the source plate used in the mapping.

getParent() - Method in class net.sf.basedb.core.Directory

Get the parent directory of this directory.

getParent() - Method in class net.sf.basedb.core.MeasuredBioMaterial

Get the parent biomaterial if there is a single parent item only.

getParent() - Method in class net.sf.basedb.core.Path

Get the parent path.

getParent() - Method in class net.sf.basedb.core.Well

Get the parent well.

getParent() - Method in interface net.sf.basedb.util.extensions.WrappingRenderer

Get the current parent renderer.

getParent() - Method in class net.sf.basedb.util.overview.Node

Get the parent of this node.

getParent() - Method in class net.sf.basedb.util.Tree.Entry

Get the entry for the parent node.

getParentBioAssay() - Method in class net.sf.basedb.core.data.RawBioAssayData

Get the derived bioassay that this raw bioassay has been created from.

getParentBioAssay() - Method in class net.sf.basedb.core.RawBioAssay

Get the DerivedBioAssay this raw bioassay is created from.

getParentExtract() - Method in class net.sf.basedb.core.data.RawBioAssayData

Get the derived bioassay that this raw bioassay has been created from.

getParentExtract() - Method in class net.sf.basedb.core.RawBioAssay

Get the Extract this raw bioassay is created from.

getParentFileSets() - Method in class net.sf.basedb.core.ArrayDesign

There are no parent file sets.

getParentFileSets() - Method in class net.sf.basedb.core.BioAssaySet

Get the file set from the parent bioassay set if it exists.

getParentFileSets() - Method in class net.sf.basedb.core.DerivedBioAssay

getParentFileSets() - Method in class net.sf.basedb.core.ExtraValue

Get the file set from the parent bioassay set if it exists.

getParentFileSets() - Method in interface net.sf.basedb.core.FileStoreEnabled

Get the file sets of parent item(s) that are related to the current item.

getParentFileSets() - Method in class net.sf.basedb.core.RawBioAssay

Get the file set from the array design, if it exists.

getParentHasNullReporter() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo

A flag that indicates if at least one position in the parent bioassay set has a null reporter or not.

getParentHasZeroReporter() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo

A flag that indicates if at least one position in the parent bioassay set has a reporter with ID=0.

getParentId() - Method in class net.sf.basedb.core.data.keyring.GroupGroups

Get the id of the parent group.

getParentInformation(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.ProtocolParameterValidator

Load parent item information from the current protocol node.

getParentItem() - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext

If the context has a parent item this method returns it.

getParentPlates() - Method in class net.sf.basedb.core.Plate

Get a query returning the parent plates of this plate.

getParentProperties(DbControl, BioAssay, Metadata.PropertyPath<RawBioAssay, ?>) - Static method in class net.sf.basedb.util.BioAssaySetUtil

Find the values of parent properties for a given bioassay.

getParentQuery() - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

Get the underlying parent query from Hibernate.

getParents() - Method in class net.sf.basedb.core.BioAssay

Get a query for loading the parents bioassays to this bioassay.

getParents() - Method in class net.sf.basedb.core.data.BioAssayData

Get a set that manages the parent bioassays the data in this bioassay is based on.

getParents() - Method in class net.sf.basedb.core.data.DerivedBioAssayData

A set that manages the parent bioassays that this derived bioassay related to.

getParents() - Method in class net.sf.basedb.core.data.GroupData

This is the inverse end.

getParents() - Method in class net.sf.basedb.core.data.ItemSubtypeData

This is the inverse end.

getParents() - Method in class net.sf.basedb.core.data.PlateData

If the plate was created by a PlateMappingData the source plates are kept here.

getParents() - Method in class net.sf.basedb.core.DerivedBioAssay

Get all parent derived bioassays.

getParents() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay

Get the parent assays of this child.

getParentSession() - Method in class net.sf.basedb.core.hibernate.SessionWrapper

Get the underlying parent session from Hibernate.

getParentSession() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

Get the underlying parent session from Hibernate.

getParentSet() - Method in class net.sf.basedb.core.data.PlateData

Duplicate of PlateData.getParents() but with a set instead of a map.

getParentSubtypes() - Method in class net.sf.basedb.core.ItemSubtype

Get a query returning all subtypes that have a relation to this subtype.

getParentSubtypes(DbControl, Subtypable, Item) - Static method in class net.sf.basedb.core.ItemSubtype

Utility method for locating all subtypes that have a relationship to the subtype of the given item.

getParentType() - Method in class net.sf.basedb.core.BasicChildItem

Get the type of item that is the parent of this item.

getParentType() - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData

Get the type of the parent item.

getParentType() - Method in class net.sf.basedb.core.ItemSubtypeFileType

getParentType() - Method in class net.sf.basedb.core.MeasuredBioMaterial

Get the item type of the parent biomaterial.

getParentType() - Method in class net.sf.basedb.core.PlatformFileType

getParentType() - Method in class net.sf.basedb.core.PlatformVariant

getParseAllExcelSheets() - Method in class net.sf.basedb.util.parser.FlatFileParser

getParsedBytes() - Method in class net.sf.basedb.util.bfs.AnnotationParser

getParsedBytes() - Method in interface net.sf.basedb.util.bfs.BfsParser

Get the number of parsed bytes so far.

getParsedBytes() - Method in class net.sf.basedb.util.bfs.DataParser

getParsedBytes() - Method in class net.sf.basedb.util.bfs.MetadataParser

getParsedBytes() - Method in class net.sf.basedb.util.charset.CharsetDetector

Get the number of bytes that the last test operation parsed.

getParsedBytes() - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser

getParsedBytes() - Method in class net.sf.basedb.util.parser.FlatFileParser

Get the number of parsed bytes so far.

getParsedCharacters() - Method in class net.sf.basedb.util.parser.FlatFileParser

Get the number of parsed characters so far.

getParsedDataLines() - Method in class net.sf.basedb.util.parser.FlatFileParser

Get the number of parsed data lines so far in the current section.

getParsedLines() - Method in class net.sf.basedb.util.charset.CharsetDetector

getParsedLines() - Method in class net.sf.basedb.util.parser.FlatFileParser

Get the number of parsed lines so far.

getParsedSections() - Method in class net.sf.basedb.util.parser.FlatFileParser

Get the number of found sections so far.

getParser() - Method in class net.sf.basedb.core.data.FormulaData

Which parser to use to convert the formula to an expression or restriction. 1 = JEP

getParser() - Method in class net.sf.basedb.core.Formula

Get the parser that converts the formula to an expresion or restriction.

getParser() - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser.SynchronizedData

The underlying parser.

getParsingFailure() - Method in class net.sf.basedb.util.charset.CharsetDetector

If the last test failed, get the exception that was thrown by the parser.

getParticipant(BioPlate) - Method in class net.sf.basedb.core.BioPlateEvent

Get the participant object representing the given bioplate in this event.

getParticipants() - Method in class net.sf.basedb.core.BioPlateEvent

Get a query returning all participants in the event.

getParticipants() - Method in class net.sf.basedb.core.data.BioPlateEventData

This is the inverse end.

getPassword() - Method in class net.sf.basedb.clients.jobagent.Agent

Get the agent.password configuration value.

getPassword() - Method in class net.sf.basedb.core.authentication.LoginRequest

Get the password to use.

getPassword() - Method in class net.sf.basedb.core.data.FileServerData

Get the password that is used to login to the server.

getPassword() - Method in class net.sf.basedb.core.data.UserData

Get the PasswordData object which allows you to change the password for the user.

getPassword() - Method in class net.sf.basedb.core.FileServer

Get the password that is used when authenticating with the file server.

getPassword() - Method in class net.sf.basedb.util.uri.ConnectionParameters

Get the password that should be used to authenticate the user.

getPasswordField() - Method in interface net.sf.basedb.clients.web.extensions.login.LoginFormAction

Get attributes for the password field on the form.

getPasswordField() - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean

getPasswordField() - Method in class net.sf.basedb.clients.web.extensions.login.PasswordLoginFormFactory

getPasswordParameter() - Method in interface net.sf.basedb.util.zip.FilePacker

The default implementation return a parameter asking for a password.

getPasswordParameter() - Method in class net.sf.basedb.util.zip.ZipFilePacker

Get the encyption password parameter.

getPath() - Method in class net.sf.basedb.core.Directory

Get the complete path to this directory.

getPath() - Method in class net.sf.basedb.core.File

Get the complete path of this file.

getPath() - Method in class net.sf.basedb.core.Metadata.BasicData2ItemPropertyPath

getPath() - Method in class net.sf.basedb.core.Metadata.BasicItem2DataPropertyPath

getPath() - Method in class net.sf.basedb.core.Metadata.CollectionPropertyPath

getPath() - Method in class net.sf.basedb.core.Metadata.CombinedPropertyPath

getPath() - Method in class net.sf.basedb.core.Metadata.ComponentPropertyPath

getPath() - Method in class net.sf.basedb.core.Metadata.DateCopyPropertyPath

getPath() - Method in class net.sf.basedb.core.Metadata.EntityPropertyPath

getPath() - Method in class net.sf.basedb.core.Metadata.EvictPropertyPath

getPath() - Method in class net.sf.basedb.core.Metadata.IdentifierPropertyPath

getPath() - Method in class net.sf.basedb.core.Metadata.MapPropertyPath

getPath() - Method in class net.sf.basedb.core.Metadata.NoopPropertyPath

getPath() - Method in interface net.sf.basedb.core.Metadata.PropertyPath

Get the path that this object represents.

getPath() - Method in class net.sf.basedb.core.Metadata.ReporterScore2DataPropertyPath

getPathInfo() - Method in class net.sf.basedb.clients.web.extensions.RequestWrapper

From the HttpServletRequestInterface ------------------------------------

getPathType() - Method in class net.sf.basedb.core.PathParameterType

Get the type of the path to ask for.

getPattern(String) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

getPattern(String, int, int) - Method in class net.sf.basedb.util.export.spotdata.AdvancedFieldConverter

getPattern(ParameterValues, String) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

getPercent() - Method in class net.sf.basedb.core.SimpleProgressReporter

Get the last percentage completed of the task.

getPercentComplete() - Method in class net.sf.basedb.core.data.JobData

If the job is running, how many percent has been completed.

getPercentComplete() - Method in class net.sf.basedb.core.Job

An estimate of the percentage of the work currently completed by an executing job.

getPercentile(List<? extends Number>, int) - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet

Calculates the percentile values from a sorted list of values.

getPermanentSelects() - Method in class net.sf.basedb.core.AbstractQuery

Get all permanent selects.

getPermission() - Method in class net.sf.basedb.core.data.keyring.KeyPermission

Get the permission.

getPermission() - Method in class net.sf.basedb.core.data.keyring.ProjectPermission

Get the permission.

getPermissionCode(Set<Permission>) - Static method in class net.sf.basedb.clients.web.PermissionUtil

Translate the given set of permissions to an integer code that can be used to later recreate the set again.

getPermissionForUse() - Method in class net.sf.basedb.core.ChildItem

Get the permission that is required on the parent item that gives use permission on the child item.

getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.BasicChildItem

Get the permission that is required on the parent item that gives write, delete and create permission on the child item.

getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.BioAssay

USE permission is enough to be able to manage bioassays.

getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.BioAssaySet

USE permission is enough to be able to manage bioassay sets.

getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.ChildItem

Get the permission that is required on the parent item that gives write, delete and create permission on the child item.

getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.DataCube

USE permission is enough to be able to manage data cubes.

getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.DataCubeColumn

USE permission is enough to be able to manage data cubes.

getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.DataCubeExtraValue

USE permission is enough to be able to manage data cubes.

getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.DataCubeFilter

USE permission is enough to be able to manage data cubes.

getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.DataCubeLayer

USE permission is enough to be able to manage data cubes.

getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.ExtraValue

USE permission is enough to be able to manage extra values.

getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.RootRawBioAssay

WRITE permission is required to be able to manage root raw bioassays.

getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.Transformation

USE permission is enough to be able to manage transformations.

getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.VirtualDb

USE permission is enough to be able to manage virtual db.

getPermissionGroups() - Static method in class net.sf.basedb.clients.web.PermissionUtil

getPermissions() - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

getPermissions() - Method in interface net.sf.basedb.core.AccessControlled

Get the logged in user's permissions on the item.

getPermissions() - Method in class net.sf.basedb.core.BasicBatcher

getPermissions() - Method in class net.sf.basedb.core.BasicItem

getPermissions() - Method in class net.sf.basedb.core.BioMaterialEventSource

getPermissions() - Method in class net.sf.basedb.core.Coloring

getPermissions() - Method in class net.sf.basedb.core.data.PluginDefinitionData

Get a map containing the rolekey and the permissions for this plugin.

getPermissions() - Method in class net.sf.basedb.core.plugin.AbstractPlugin

Return null, which gives the plugin the same permissions as the logged in user.

getPermissions() - Method in interface net.sf.basedb.core.plugin.Plugin

Get the permissions this plugin requires to function as expected.

getPermissions() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter

Request read access to File:s, read access to annotation types and write access to all annotatable items.

getPermissions() - Method in class net.sf.basedb.plugins.Base1PluginExecuter

getPermissions() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin

Request create and write access to File:s and Directory:s and read access to Experiment:s and User:s.

getPermissions() - Method in class net.sf.basedb.plugins.CdfFileReporterImporter

Request create and write access to Reporter:s and read access to File:s ArrayDesign:s, ReporterType:s, Platform:s and DataFileType:s

getPermissions() - Method in class net.sf.basedb.plugins.CloneReportersPlugin

Request write permission to Experiment:s and Reporter clone templates and read permission to reporters.

getPermissions() - Method in class net.sf.basedb.plugins.FormulaFilter

Request use access to Experiment:s and read access to Job:s and ReporterLists.

getPermissions() - Method in class net.sf.basedb.plugins.GalExporter

Request create and write access to File:s, Directory:s and ArrayDesign:s read access to User:s and forced read access to DataFileType:s.

getPermissions() - Method in class net.sf.basedb.plugins.HelpExporter

Request create and write access to File:s and Directory:s and read access to Client:s and User:s.

getPermissions() - Method in class net.sf.basedb.plugins.HelpImporter

Request write access to Client:s and read access to File:s.

getPermissions() - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin

Request use access to Experiment:s and read access to RawBioAssay:s, ArrayDesign:s, Formulas:s, Job:s and and Reporter:s.

getPermissions() - Method in class net.sf.basedb.plugins.JepExtraValueCalculator

Request use access to Experiment:s and ExtraValueType:s and read access to Job:s.

getPermissions() - Method in class net.sf.basedb.plugins.JepIntensityTransformer

Request use access to Experiment:s and read access to Job:s.

getPermissions() - Method in class net.sf.basedb.plugins.LowessNormalization

Request use access to Experiment:s and read access to Job:s.

getPermissions() - Method in class net.sf.basedb.plugins.MedianRatioNormalization

Request use access to Experiment:s and read access to Job:s.

getPermissions() - Method in class net.sf.basedb.plugins.PackedFileExporter

Request create and delete access to File:s and Directory:s.

getPermissions() - Method in class net.sf.basedb.plugins.PlateFlatFileImporter

Request create access to Plate:s, use access to PlateType:s and read access to Reporter:s, PlateGeometry:s and File:s.

getPermissions() - Method in class net.sf.basedb.plugins.PlateMappingExporter

Request create and write access to File:s and Directory:s and read access to PlateMapping:s and PlateGeometries.

getPermissions() - Method in class net.sf.basedb.plugins.PlateMappingImporter

Request create and write access to PlateMapping:s, create and use access to PlateGeometries and read access to File:s.

getPermissions() - Method in class net.sf.basedb.plugins.PluginConfigurationExporter

Request create and write access to File:s and Directory:s and read access to PluginConfigurations:s, PluginDefinition:s and User:s.

getPermissions() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter

Request write access to ArrayDesign:s, read access to Plate:s, Reporter:s, DataFileType:s, Platform:s and File:s.

getPermissions() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter

Request write access to RawBioAssay:s and read access to ArrayDesign:s, File:s, Reporter:s, Platform:s and DataFileType:s

getPermissions() - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter

Request create, write and delete access to Reporter:s, write access to ReporterList:s and read access to File:s and ReporterType:s.

getPermissions() - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

Request write access to ArrayDesign:s, read access to Reporter:s, DataFileType:s, Platform:s and File:s.

getPermissions() - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker

Request create and write access to File:s and Directory:s.

getPermissions(int) - Static method in class net.sf.basedb.clients.web.PermissionUtil

Translate a given integer to a set of permissions.

getPermissions(Group) - Method in class net.sf.basedb.core.GroupPermissions

Get the permissions for a group.

getPermissions(Group) - Method in class net.sf.basedb.core.ItemKey

Get the permissions for a group.

getPermissions(Group) - Method in class net.sf.basedb.core.MultiPermissions

Get the permissions for a group.

getPermissions(Group) - Method in class net.sf.basedb.core.Project

Get the permissions for a group in this project.

getPermissions(Project) - Method in class net.sf.basedb.core.MultiPermissions

Get the permissions for a project.

getPermissions(Project) - Method in class net.sf.basedb.core.ProjectKey

Get the permissions for a project.

getPermissions(Project) - Method in class net.sf.basedb.core.ProjectPermissions

Get the permissions for a project.

getPermissions(Role) - Method in class net.sf.basedb.core.RoleKey

Get the permissions for a role.

getPermissions(User) - Method in class net.sf.basedb.core.ItemKey

Get the permissions for a user.

getPermissions(User) - Method in class net.sf.basedb.core.MultiPermissions

Get the permissions for a user.

getPermissions(User) - Method in class net.sf.basedb.core.Project

Get the permissions for a user in this project.

getPermissions(User) - Method in class net.sf.basedb.core.UserPermissions

Get the permissions for a user.

getPermissionTemplate() - Method in class net.sf.basedb.core.data.ProjectData

A permission template can be used to set default permissions when this project is active.

getPermissionTemplate() - Method in class net.sf.basedb.core.Project

Get the permission template that is used to share new items when this project is active.

getPhone() - Method in class net.sf.basedb.core.authentication.ExtraUserInformation

The phone number to the user.

getPhone() - Method in class net.sf.basedb.core.data.UserData

Get the phone number to the user, or null if unknown.

getPhone() - Method in class net.sf.basedb.core.User

Get the phone number to the user, or null if unknown.

getPhysicalBioAssay() - Method in class net.sf.basedb.core.ArraySlide

Get the PhysicalBioAssay item which was used on this slide.

getPhysicalBioAssay() - Method in class net.sf.basedb.core.BioMaterialEvent

Get the PhysicalBioAssay that was created by this event.

getPhysicalBioAssay() - Method in class net.sf.basedb.core.data.ArraySlideData

Get the bioassay.

getPhysicalBioAssay() - Method in class net.sf.basedb.core.data.BioMaterialEventData

Get the physical bioassay that was created by this event.

getPhysicalBioAssays() - Method in class net.sf.basedb.core.data.DerivedBioAssayData

A set that manages the parent physical bioassays that this derived bioassay is related to.

getPhysicalBioAssays() - Method in class net.sf.basedb.core.DerivedBioAssay

Get a query that returns the physical bioassays used to create this derived bioassay.

getPhysicalBioAssays() - Method in class net.sf.basedb.core.Extract

Get a query that returns all bioassays created from this extract.

getPhysicalBioAssays(DbControl, OverviewContext, DerivedBioAssay) - Static method in class net.sf.basedb.util.overview.validator.PhysicalBioAssayValidator

Get all physical bioassays that are parents to the given derived bioassay.

getPlaceHolder() - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo

Get a placeholder text that is displayed in the field when it is empty.

getPlainConnection() - Static method in class net.sf.basedb.core.HibernateUtil

getPlate() - Method in class net.sf.basedb.core.ArrayDesignPlate

Gets the Plate that belongs to this item.

getPlate() - Method in class net.sf.basedb.core.BioWell

Get the BioPlate this biowell belongs to.

getPlate() - Method in class net.sf.basedb.core.data.ArrayDesignPlateData

Get the Plate.

getPlate() - Method in class net.sf.basedb.core.data.MappingCoordinate

Get the plate number.

getPlate() - Method in class net.sf.basedb.core.data.PlateEventData

The plate this event belongs to.

getPlate() - Method in class net.sf.basedb.core.data.WellData

The plate this well belongs to.

getPlate() - Method in class net.sf.basedb.core.PlateEvent

Get the Plate this event belongs to.

getPlate() - Method in class net.sf.basedb.core.Well

Get the Plate this event belongs to.

getPlate(int) - Method in class net.sf.basedb.core.ArrayDesign

Get a Plate from a given position.

getPlateCoordinate() - Method in class net.sf.basedb.core.BioWell

Get the plate coordinate representation of the coordinate for this well.

getPlateEvents() - Method in class net.sf.basedb.core.data.PlateEventTypeData

This is the inverse end.

getPlateEventType() - Method in class net.sf.basedb.core.data.PlateEventData

The event type of this event.

getPlateEventType() - Method in class net.sf.basedb.core.PlateEvent

Get the PlateEventType of this event.

getPlateGeometry() - Method in class net.sf.basedb.core.BioPlate

Get the PlateGeometry of this bioplate.

getPlateGeometry() - Method in class net.sf.basedb.core.data.BioPlateData

The geometry of this plate type.

getPlateGeometry() - Method in class net.sf.basedb.core.data.PlateTypeData

The geometry of this plate type.

getPlateGeometry() - Method in class net.sf.basedb.core.PlateType

Get the PlateGeometry of this plate type.

getPlateMapping() - Method in class net.sf.basedb.core.data.PlateData

If this plate was created by a plate mapping, it is linked here.

getPlateMapping() - Method in class net.sf.basedb.core.Plate

Get the PlateMapping used to create this plate.

getPlatePosition(Plate) - Method in class net.sf.basedb.core.ArrayDesign

Get the position of a Plate in this array design.

getPlates() - Method in class net.sf.basedb.core.ArrayDesign

Get a query that returns the plates that are used by this arraydesign.

getPlates() - Method in class net.sf.basedb.core.data.ArrayDesignData

The plates this design is made from.

getPlates() - Method in class net.sf.basedb.core.data.PlateTypeData

The plates of this type.

getPlates() - Method in class net.sf.basedb.core.PlateType

Get a query that returns all plates of this plate type.

getPlateType() - Method in class net.sf.basedb.core.data.PlateData

The plate type of this plate.

getPlateType() - Method in class net.sf.basedb.core.data.PlateEventTypeData

The plate type this event type belongs to.

getPlateType() - Method in class net.sf.basedb.core.Plate

Get the PlateType of this plate.

getPlateType() - Method in class net.sf.basedb.core.PlateEventType

Get the PlateType this event type belongs to.

getPlateTypes() - Method in class net.sf.basedb.core.data.PlateGeometryData

This is the invers end.

getPlateTypes() - Method in class net.sf.basedb.core.PlateGeometry

Get a query returning all plate types using this geometry.

getPlatform() - Method in class net.sf.basedb.core.ArrayDesign

getPlatform() - Method in class net.sf.basedb.core.BioAssaySet

getPlatform() - Method in class net.sf.basedb.core.data.ArrayDesignData

Get the platform this raw bioassay uses

getPlatform() - Method in class net.sf.basedb.core.data.PlatformFileTypeData

Get the platform.

getPlatform() - Method in class net.sf.basedb.core.data.PlatformVariantData

The parent platform of this variant.

getPlatform() - Method in class net.sf.basedb.core.data.RawBioAssayData

Get the platform this raw bioassay uses.

getPlatform() - Method in class net.sf.basedb.core.DerivedBioAssay

getPlatform() - Method in class net.sf.basedb.core.ExtraValue

getPlatform() - Method in interface net.sf.basedb.core.FileStoreEnabled

Get the platform the item is related to.

getPlatform() - Method in class net.sf.basedb.core.PlatformFileType

Get the platform.

getPlatform() - Method in class net.sf.basedb.core.PlatformVariant

Get that platform this is a variant of.

getPlatform() - Method in class net.sf.basedb.core.RawBioAssay

getPlatform(DbControl) - Method in class net.sf.basedb.core.RawDataType

Get the platform that this raw data type is associated with.

getPlatformRawDataType(Session, String) - Static method in class net.sf.basedb.core.RawDataTypes

getPlatforms() - Method in class net.sf.basedb.core.data.DataFileTypeData

This is the inverse end.

getPlatforms() - Method in class net.sf.basedb.core.DataFileType

Get a query that returns all platforms/variants that are using this file type.

getPlotGenerators() - Method in interface net.sf.basedb.clients.web.extensions.plot.OverviewPlotAction

The plot generates that contains information for each image that is generated.

getPlotGenerators() - Method in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean

getPlugin() - Method in class net.sf.basedb.core.data.ChangeHistoryData

getPlugin() - Method in class net.sf.basedb.core.PluginRequest

Get the plugin object.

getPlugin(DbControl) - Method in class net.sf.basedb.core.ChangeHistory

Load the plug-in that made the change.

getPlugin(DbControl) - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo

Load the plug-in that was executing the transaction.

getPlugin(DbControl, ChangeHistory, boolean, boolean) - Static method in class net.sf.basedb.clients.web.ChangeHistoryUtil

Get the plug-in that made the change in HTML format.

getPluginConfiguration() - Method in class net.sf.basedb.core.data.JobData

The plugin configuration for the plugin.

getPluginConfiguration() - Method in class net.sf.basedb.core.Job

Get the PluginConfiguration defining the plugin this job should execute.

getPluginConfiguration() - Method in class net.sf.basedb.core.ParameterValuesImpl

getPluginConfiguration() - Method in class net.sf.basedb.core.plugin.NamespaceParameterValuesWrapper

getPluginConfiguration() - Method in interface net.sf.basedb.core.plugin.ParameterValues

Get the configuration that we are using/configuring.

getPluginConfiguration() - Method in class net.sf.basedb.core.plugin.ParameterValuesWrapper

getPluginConfiguration() - Method in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues

getPluginConfiguration() - Method in class net.sf.basedb.util.ContextUtil.ContextResult

Get the plugin configuration that was checked, or null.

getPluginConfigurations() - Method in class net.sf.basedb.core.PluginDefinition

Get a query that returns the configurations for this plugin definition.

getPluginDefinition() - Method in class net.sf.basedb.core.data.JobAgentSettingsData

The plugin these settings are used for.

getPluginDefinition() - Method in class net.sf.basedb.core.data.JobData

The plugin that executes the job.

getPluginDefinition() - Method in class net.sf.basedb.core.data.PluginConfigurationData

Get the plugin definition for this configuration.

getPluginDefinition() - Method in class net.sf.basedb.core.Job

Get the PluginConfiguration defining the plugin this job should execute.

getPluginDefinition() - Method in class net.sf.basedb.core.JobAgentSettings

Get the plugin that these settings are used for.

getPluginDefinition() - Method in class net.sf.basedb.core.ParameterValuesImpl

getPluginDefinition() - Method in class net.sf.basedb.core.plugin.NamespaceParameterValuesWrapper

getPluginDefinition() - Method in interface net.sf.basedb.core.plugin.ParameterValues

Get the plugin that we are executing/configuring.

getPluginDefinition() - Method in class net.sf.basedb.core.plugin.ParameterValuesWrapper

Get the PluginDefinition of either the job or the configuration, depending in the preferJob parameter that was set when creating this object.

getPluginDefinition() - Method in class net.sf.basedb.core.PluginConfiguration

Get the plugin definition for this configuration.

getPluginDefinition() - Method in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues

getPluginDefinition() - Method in class net.sf.basedb.util.ContextUtil.ContextResult

Get the plugin definition that was checked.

getPluginDefinitionId() - Method in class net.sf.basedb.core.data.keyring.PluginKeys

Gets the id of the plugin

getPluginDefinitions() - Method in class net.sf.basedb.util.extensions.xml.XmlLoader

Get a list with all loaded plug-in definitions.

getPluginDirectory(DbControl, String) - Method in class net.sf.basedb.plugins.Base1PluginExecuter

Get a directory

getPluginId() - Method in class net.sf.basedb.core.ChangeHistory

Get the ID of the plug-in that was making the change.

getPluginId() - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo

Get the ID of the plug-in that was executing the transaction.

getPluginId() - Method in class net.sf.basedb.core.data.ChangeHistoryData

The ID of the plug-in that was making the changes.

getPluginId() - Method in class net.sf.basedb.core.log.TransactionDetails

Get the ID of the currently running plug-in or 0 if no plug-in is running.

getPluginId() - Method in class net.sf.basedb.core.SessionControl

Get the id of the plug-in that is currently running with this session control.

getPluginName() - Method in class net.sf.basedb.core.log.TransactionDetails

Utility method for loading the name of the currently executing plugin.

getPluginName() - Method in class net.sf.basedb.core.SessionControl

Get the name of the plug-in that is currently running with this session control.

getPluginParameter() - Method in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter

getPluginPermissions() - Method in class net.sf.basedb.core.Annotation

getPluginPermissions() - Method in class net.sf.basedb.core.AnnotationSet

getPluginPermissions() - Method in class net.sf.basedb.core.AnyToAny

getPluginPermissions() - Method in class net.sf.basedb.core.BasicBatcher

getPluginPermissions() - Method in class net.sf.basedb.core.BasicChildItem

getPluginPermissions() - Method in class net.sf.basedb.core.BasicItem

getPluginPermissions() - Method in class net.sf.basedb.core.ChildItem

getPluginPermissions() - Method in class net.sf.basedb.core.FeatureBatcher

getPluginPermissions() - Method in class net.sf.basedb.core.FileSet

getPluginPermissions() - Method in class net.sf.basedb.core.FileSetMember

getPluginPermissions() - Method in class net.sf.basedb.core.ItemKey

getPluginPermissions() - Method in class net.sf.basedb.core.Project

Make sure plug-ins always has at least read access to the active project.

getPluginPermissions() - Method in class net.sf.basedb.core.ProjectKey

getPluginPermissions() - Method in class net.sf.basedb.core.RawDataBatcher

getPluginPermissions() - Method in class net.sf.basedb.core.ReporterCloneTemplate

getPluginPermissions() - Method in class net.sf.basedb.core.RoleKey

getPluginPermissions() - Method in class net.sf.basedb.core.User

Make sure plug-ins always has at least read access to the logged in user.

getPluginPermissions(Item) - Method in class net.sf.basedb.core.Keyring

Get the active plugin's permissions to an unspecified item of a certain Item type.

getPluginPermissions(Item) - Method in class net.sf.basedb.core.SessionControl

Get all plugin-specific permissions for the specified item type.

getPlugins() - Method in class net.sf.basedb.core.data.JobAgentData

The plugins that can be executed by this job agent.

getPlugins() - Method in class net.sf.basedb.core.data.PluginTypeData

The plugin implementing this interface.

getPlugins() - Method in class net.sf.basedb.core.PluginType

Get a query that returns the plugin definitions which implements this type.

getPluginsDir() - Method in class net.sf.basedb.clients.web.extensions.XJspCompiler

Get the path to the plug-in directory from BASE.

getPluginsDirectory() - Static method in class net.sf.basedb.core.Application

Get the directory where plug-ins and extensions must be installed.

getPluginSessionControl(PluginDefinition, Job) - Method in class net.sf.basedb.core.PluginSessionControl

Create a new session control for executing a plugin using the same parent as this session control has.

getPluginSessionControl(PluginDefinition, Job) - Method in class net.sf.basedb.core.SessionControl

Create a new session control for executing a plugin.

getPluginTypes() - Method in class net.sf.basedb.core.data.PluginDefinitionData

The plugin types of this plugin, ie. all interfaces that it implements.

getPluginTypes() - Method in class net.sf.basedb.core.PluginDefinition

Get a query that returns the plugin types for this plugin definition.

getPluginVersion() - Method in class net.sf.basedb.core.data.JobData

Get the version of the plugin used to execute this job at the time the job was executed or registered.

getPluginVersion() - Method in class net.sf.basedb.core.Job

Get the version of the plugin used to execute this job at the time the job was executed or registered.

getPort() - Method in class net.sf.basedb.clients.jobagent.Agent

Get the agent.port configuration value.

getPort() - Method in class net.sf.basedb.core.data.JobAgentData

The port the job agent is listening on. null if it doesn't listen.

getPort() - Method in class net.sf.basedb.core.JobAgent

Get the port the job agent is listening on.

getPosition() - Method in class net.sf.basedb.core.ArrayDesignPlate

Gets the position of this item.

getPosition() - Method in class net.sf.basedb.core.BioMaterialEventSource

Get the position that the source biomaterial was used on in the event.

getPosition() - Method in class net.sf.basedb.core.BioPlate

Get the position within the "storage location" for this bioplate.

getPosition() - Method in class net.sf.basedb.core.data.ArrayDesignPlateData

Get the index.

getPosition() - Method in class net.sf.basedb.core.data.BioMaterialEventSourceData

Get the position of the parent biomaterial as it was used in the event.

getPosition() - Method in class net.sf.basedb.core.data.BioPlateData

Get the position in the storage location were the bioplate is stored.

getPosition() - Method in class net.sf.basedb.core.data.FeatureData

Get the position number of the feature.

getPosition() - Method in class net.sf.basedb.core.data.RawData

getPosition() - Method in class net.sf.basedb.core.RawDataBatcher.FeatureInfo

getPosition() - Method in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter

getPosition(DbControl, int, int) - Method in class net.sf.basedb.clients.web.ExperimentExplorer

Get the position number of the position specified by the given reporter and position index.

getPositionBatcher() - Method in class net.sf.basedb.core.BioAssaySet

Get a batcher that links position coordinates to reporters for the data cube this bioassayset uses.

getPositionBatcher() - Method in class net.sf.basedb.core.DataCube

getPositionData() - Method in class net.sf.basedb.core.BioAssaySet

Get a query that returns position data for the data cube where this bioassayset is located.

getPositionExtraValueBatcher(Class<I>, ExtraValueType, Job) - Method in class net.sf.basedb.core.BioAssaySet

Get a batcher that is used to insert extra values per position of the specified type.

getPositionIndex() - Method in class net.sf.basedb.clients.web.ExperimentExplorer

Get the index of the current position.

getPositionIndex() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo

The index of the 'position' data column.

getPredefinedQuery(Session, String) - Static method in class net.sf.basedb.core.HibernateUtil

Get a predefined HQL query.

getPredefinedQuery(Session, String, Class<R>, String...) - Static method in class net.sf.basedb.core.HibernateUtil

Get a predefined HQL query with a known return type.

getPredefinedQuery(Session, String, String...) - Static method in class net.sf.basedb.core.HibernateUtil

Get a predefined HQL query.

getPredefinedQuery(StatelessSession, String, Class<R>) - Static method in class net.sf.basedb.core.HibernateUtil

Get a predefined HQL query with a known return type using the stateless session.

getPredefinedSQLQuery(Session, String, Class<R>, String...) - Static method in class net.sf.basedb.core.HibernateUtil

Get a predefined SQL query with a known return type.

getPredefinedSQLQuery(Session, String, String...) - Static method in class net.sf.basedb.core.HibernateUtil

Get a predefined SQL query.

getPredefinedSQLQuery(StatelessSession, String) - Static method in class net.sf.basedb.core.HibernateUtil

Get a predefined SQL query using the stateless session.

getPredefinedSQLQuery(StatelessSession, String, Class<R>) - Static method in class net.sf.basedb.core.HibernateUtil

Get a predefined SQL query with a known return type using the stateless session.

getPrefix() - Method in class net.sf.basedb.clients.web.taglib.table.CellValue

getPrefix() - Method in class net.sf.basedb.util.bfs.SequenceFilenameGenerator

Get the prefix that is used for file name generation.

getPrefixedStream(XlsxToCsvUtil.SheetInfo) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.WorkbookStream

Create a combined stream by adding a "prefix": [sheet-name] and then the regular CSV stream for the given worksheet.

getPreset(String) - Method in class net.sf.basedb.core.Presets

Get a named preset.

getPreviousState() - Method in class net.sf.basedb.core.log.EntityDetails

Get an array with the previous state of the entity.

getPrimaryKey() - Method in class net.sf.basedb.core.dbengine.TableInfo

Get information about the primary key of the table

getPrintRobot() - Method in class net.sf.basedb.core.ArrayBatch

Get the print robot used for printing the arrays.

getPrintRobot() - Method in class net.sf.basedb.core.data.ArrayBatchData

Get the hardware used for creating this batch.

getPriority() - Method in class net.sf.basedb.core.data.JobData

The jobs priority.

getPriority() - Method in class net.sf.basedb.core.Job

Get the priority of the job.

getPriorityBoost() - Method in class net.sf.basedb.core.data.JobAgentSettingsData

The priority boost for this plugin.

getPriorityBoost() - Method in class net.sf.basedb.core.JobAgentSettings

Get the priority boost given to jobs executed by this plugin.

getPrivateKey(String) - Method in class net.sf.basedb.util.ssl.StaticKeyManager

getProcessResults() - Method in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor

getProcessResults() - Method in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor

getProcessResults() - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor

getProducer() - Method in class net.sf.basedb.core.hibernate.QueryWrapper

getProducts() - Method in class net.sf.basedb.core.data.TransformationData

This is the inverse end.

getProducts() - Method in class net.sf.basedb.core.Transformation

Get a query that return all bioassaysets created by this transformation.

getProgramParameters() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

Get all program parameters and their values.

getProgress() - Method in class net.sf.basedb.clients.web.fileupload.FileUpload

Get progress information about the upload.

getProgress(FlatFileParser) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

Get the progress of import as a percentage value.

getProgress(FlatFileParser) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter

Overriding default implementation since we want file parsing to only use 'progressParser'% and the remaining 'progressDatabase'% for storing to the database.

getProgressReporter() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

Get the progress reporter

getProgressReporter() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter

Get the progress reporter.

getProgressReporter() - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter

Get the progress reporter.

getProgressReporter(ProgressReporter) - Method in class net.sf.basedb.core.Job

Get a progress reporter that reports progress by updating the information in the database.

getProject() - Method in class net.sf.basedb.core.Annotation

Get the project that this project-specific annotation belongs to.

getProject() - Method in class net.sf.basedb.core.data.ChangeHistoryData

getProject() - Method in class net.sf.basedb.util.overview.GenericOverview

Get the project of this overview is using for validating against project defaults (may be null).

getProject() - Method in interface net.sf.basedb.util.overview.OverviewContext

Get the project the overview is using as the "current" project.

getProject(DbControl) - Method in class net.sf.basedb.core.ChangeHistory

Load the project that was active when the change was made.

getProject(DbControl) - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo

Load the project that was active during the transaction.

getProject(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

Get the project that a project-specific annotation belongs to.

getProject(DbControl, ChangeHistory, boolean, boolean) - Static method in class net.sf.basedb.clients.web.ChangeHistoryUtil

Get the project that was active when the change was made in HTML format.

getProjectAnnotation(AnnotationType, Project) - Method in class net.sf.basedb.core.AnnotationSet

Get a value for a project-specific annotation using the specified project instead of the currently active project.

getProjectAnnotations() - Method in class net.sf.basedb.core.AnnotationType

If this flag is set, annotation values can be set per project.

getProjectAnnotations() - Method in class net.sf.basedb.core.data.AnnotationTypeData

If this flag is set, annotation values can be set per project.

getProjectAnnotations(Annotation.Source, Project) - Method in class net.sf.basedb.core.AnnotationSet

Get a query returning annotations with the specified source and belonging to the specified project (or default values if projectId=0).

getProjectDefaultPlatform(DbControl) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Get the default platform of the currently active project.

getProjectDefaultRawDataType(DbControl) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Get the default raw data type of the currently active project.

getProjectDefaults() - Method in class net.sf.basedb.core.data.ProjectData

Gets the default values

getProjectDefaultVariant(DbControl) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Get the default platform variant of the currently active project.

getProjectId() - Method in class net.sf.basedb.core.Annotation

Get the ID of the project that this project-specicif annotation belongs to.

getProjectId() - Method in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo

Get the id of the project this annotation belong to.

getProjectId() - Method in class net.sf.basedb.core.ChangeHistory

Get the ID of the project that was active when the change was made.

getProjectId() - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo

Get the ID of the project that was active during the transaction.

getProjectId() - Method in class net.sf.basedb.core.data.AnnotationData

The ID of the project that this annotation belongs to. 0 is used for default annotations.

getProjectId() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink

getProjectId() - Method in class net.sf.basedb.core.data.ChangeHistoryData

The ID of the project that was active when the changes were made.

getProjectId() - Method in class net.sf.basedb.core.data.keyring.ProjectKeys

Get the id of the project.

getProjectId() - Method in class net.sf.basedb.core.data.keyring.ProjectPermission

Get the id of the project.

getProjectId() - Method in class net.sf.basedb.core.log.TransactionDetails

Get the ID of the currently active project, or 0 if no project is active.

getProjectId() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

Get the id of the project that this project-specific annotation belongs to.

getProjectIds(Permission) - Method in class net.sf.basedb.core.ProjectKey

Get the ID:s of all projects that are shared with this project key having the specified permission.

getProjectKey() - Method in interface net.sf.basedb.core.data.ShareableData

Get the ProjectKeyData for the item.

getProjectKey() - Method in class net.sf.basedb.core.data.SharedData

getProjectKey() - Method in interface net.sf.basedb.core.Shareable

Get the ProjectKey that is used to share this item to projects.

getProjectKey() - Method in class net.sf.basedb.core.SharedItem

getProjectKeyId() - Method in class net.sf.basedb.core.SessionControl

Get the id of the ProjectKey that can be used to share an item to the active project with full permission, or 0 if no project is active or the logged in user only has read permission to the active project.

getProjectKeys() - Method in class net.sf.basedb.core.data.ProjectData

This is the inverse end.

getProjectKeys() - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring

Return empty set.

getProjectKeys() - Method in class net.sf.basedb.core.Job.SignalKeyring

Return empty set.

getProjectKeys() - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring

Return empty set.

getProjectKeys() - Method in class net.sf.basedb.core.SessionControl

Get the id of all project keys where the logged in user has read permission.

getProjectKeys(Permission) - Method in class net.sf.basedb.core.Keyring

getProjectKeys(Permission) - Method in class net.sf.basedb.core.SessionControl

Get the id of all project keys where the logged in user has the requested permission.

getProjectName() - Method in class net.sf.basedb.core.log.TransactionDetails

Utility method for loading the name of the currently active project.

getProjectName(int) - Method in class net.sf.basedb.core.log.TransactionDetails

Get the name of the project with the given id.

getProjectName(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

Get the name of project if the annotation is a project-specific value.

getProjectPermission(Project) - Method in class net.sf.basedb.core.SessionControl

getProjectPermissions() - Method in class net.sf.basedb.core.ProjectPermissions

Get the internal representation of the permissions.

getProjects() - Method in class net.sf.basedb.core.data.GroupData

This is the inverse end.

getProjects() - Method in class net.sf.basedb.core.data.PermissionTemplateData

This is the inverse end.

getProjects() - Method in class net.sf.basedb.core.data.ProjectKeyData

Get the map that manages which projects that have permissions for this key.

getProjects() - Method in class net.sf.basedb.core.data.UserData

This is the inverse end.

getProjects() - Method in class net.sf.basedb.core.Group

Get a query that returns the projects that this group is a member of.

getProjects() - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring

Return empty map.

getProjects() - Method in class net.sf.basedb.core.Job.SignalKeyring

Return empty map.

getProjects() - Method in class net.sf.basedb.core.Keyring

getProjects() - Method in class net.sf.basedb.core.MultiPermissions

Get a query that returns all projects appearing in at least one of the project keys.

getProjects() - Method in class net.sf.basedb.core.PermissionTemplate

Get a query that returns all projects that use this permission template.

getProjects() - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring

Return empty map.

getProjects() - Method in class net.sf.basedb.core.SessionControl

Get the id of all projects where the logged in user is a member, directly or indirectly.

getProjects() - Method in class net.sf.basedb.core.User

Get a query that returns the projects where this user is a member.

getProjectSpecificAnnotationsManager() - Method in class net.sf.basedb.core.DbControl

Get the manager used for handling project specific annotations in this transaction.

getPrompt() - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo

Get the prompt that is associated with the field.

getProperties() - Method in class net.sf.basedb.core.data.ReporterCloneTemplateData

Get the map that manages cloned properties.

getProperties() - Method in class net.sf.basedb.core.hibernate.SessionWrapper

getProperties() - Method in class net.sf.basedb.core.log.EntityDetails

Get an array with the names of all properties.

getProperties() - Method in class net.sf.basedb.core.RawDataType

Get a list of RawDataProperty:s with definitions for the extra properties that has been defined for this raw data type.

getProperties(String) - Static method in class net.sf.basedb.core.ExtendedProperties

Get a list of extended properties for the specified class.

getProperties(String, boolean) - Static method in class net.sf.basedb.core.ExtendedProperties

Get a list of extended properties for the specified class.

getProperty() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

getProperty() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction

The property name for referencing data in the column.

getProperty() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

Get the property from the expression.

getProperty() - Method in class net.sf.basedb.clients.web.taglib.PropertyValue

getProperty() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

getProperty() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn

getProperty() - Method in class net.sf.basedb.core.PropertyFilter

Get the name of the property this filter is used on.

getProperty() - Method in class net.sf.basedb.plugins.batchimport.PropertyIdMethod

getProperty() - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField

Get the configured property.

getProperty(String) - Method in class net.sf.basedb.clients.jobagent.Agent

Get a configuration property.

getProperty(String) - Method in class net.sf.basedb.core.RawDataType

getProperty(String) - Method in class net.sf.basedb.util.extensions.xml.PluginInfo

getProperty(String, String) - Static method in class net.sf.basedb.core.ExtendedProperties

Find an extended property in a given class.

getPropertyAccessStrategy() - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter

getPropertyFilter(String) - Method in class net.sf.basedb.core.ItemContext

Get a filter for a property on filter row 0.

getPropertyFilter(String, int) - Method in class net.sf.basedb.core.ItemContext

Get a filter for a property.

getPropertyFilter(String, int) - Method in class net.sf.basedb.core.SyncFilter

Get a filter for a property on a given filter row.

getPropertyFilters() - Method in class net.sf.basedb.core.data.ContextData

Get the map that manages property filters in this context.

getPropertyFilters() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData

Get the map that manages property filters in this sync filter.

getPropertyFilters() - Method in class net.sf.basedb.core.ItemContext

Get a collection of all property filters stored in this context.

getPropertyFilters(int) - Method in class net.sf.basedb.core.ItemContext

Get a collection of all property filters stored in this context for a given filter row.

getPropertyFilters(int) - Method in class net.sf.basedb.core.SyncFilter

Get the filters in the given filter row.

getPropertyFilterString(PropertyFilter, Formatter<Date>) - Static method in class net.sf.basedb.clients.web.Base

Convert a property filter to a displayable string with operator + value.

getPropertyName(String) - Method in class net.sf.basedb.core.log.EntityLogOptions

Convert a method name into a property name.

getPropertyObject(String) - Method in class net.sf.basedb.core.ItemContext

getPropertyPath(Object, String) - Method in class net.sf.basedb.clients.web.taglib.PropertyValue

getPropertyPath(String, boolean) - Method in class net.sf.basedb.core.Metadata

Get a property path that can be used to retrieve a value from an item instead of using the regular get methods.

getPropertyValue(D, String) - Method in class net.sf.basedb.core.BasicBatcher

Get the value of a protected property value on a data object using Hibernate built-in reflection methods.

getPropertyValue(String) - Method in class net.sf.basedb.core.ItemContext

Get the value of a property filter on row 0.

getPropertyValue(String, int) - Method in class net.sf.basedb.core.ItemContext

Get the value of a property filter on the given filter row.

getProtocol() - Method in interface net.sf.basedb.core.Annotatable

A protcol used in the creation of an item that is used to attach annotations for the protocol parameters.

getProtocol() - Method in class net.sf.basedb.core.AnnotatedItem

Default implementation returns null.

getProtocol() - Method in class net.sf.basedb.core.ArrayBatch

Get the Protocol used for printing the arrays.

getProtocol() - Method in class net.sf.basedb.core.BioAssay

Default implementation returns null.

getProtocol() - Method in class net.sf.basedb.core.BioAssaySet

Default implementation returns null.

getProtocol() - Method in class net.sf.basedb.core.BioMaterialEvent

Get the Protocol describing the procedure used in this event.

getProtocol() - Method in class net.sf.basedb.core.BioPlateEvent

Get the Protocol describing the procedure used in this event.

getProtocol() - Method in class net.sf.basedb.core.data.ArrayBatchData

Get the protocol used for printing the arrays.

getProtocol() - Method in class net.sf.basedb.core.data.BioMaterialEventData

Get the protocol used in this event.

getProtocol() - Method in class net.sf.basedb.core.data.BioPlateEventData

Get the protocol used in this event.

getProtocol() - Method in class net.sf.basedb.core.data.DerivedBioAssayData

Get the protocol used to create this bioassay set.

getProtocol() - Method in class net.sf.basedb.core.data.PlateEventData

The protocol used for the event.

getProtocol() - Method in class net.sf.basedb.core.data.RawBioAssayData

Get the protocol used for the image analysis.

getProtocol() - Method in class net.sf.basedb.core.DerivedBioAssay

getProtocol() - Method in class net.sf.basedb.core.MeasuredBioMaterial

Get the protocol from the creation event.

getProtocol() - Method in class net.sf.basedb.core.PhysicalBioAssay

Get the protocol from the creation event.

getProtocol() - Method in class net.sf.basedb.core.PlateEvent

Get the Protocol that was followed in this event.

getProtocol() - Method in class net.sf.basedb.core.PluginDefinition

getProtocol() - Method in class net.sf.basedb.core.Project

Default implementation returns null.

getProtocol() - Method in class net.sf.basedb.core.RawBioAssay

Get the Protocol used while analysing the scanned images.

getProtocol() - Method in class net.sf.basedb.core.RootRawBioAssay

getProtocol() - Method in class net.sf.basedb.core.Well

getProtocolParametersQuery(Protocol) - Static method in class net.sf.basedb.clients.web.Base

Get a query that returns all annotation types assigned as parameters to a specific protocol.

getProtocols() - Method in class net.sf.basedb.core.data.AnnotationTypeData

This is the inverse end.

getProtocolType() - Method in class net.sf.basedb.core.data.PlateEventTypeData

The protocol type that events of this event type should pick their protocols from.

getProtocolType() - Method in class net.sf.basedb.core.PlateEventType

Get the associated protocol type item.

getProxy(int) - Static method in class net.sf.basedb.core.Reporter

Get a proxy reporter object.

getProxyTag(Annotatable) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn

Generate a proxy tag that is returned instead of actual data.

getPublication() - Method in class net.sf.basedb.core.data.ExperimentData

Get the publication for this experiment.

getPublication() - Method in class net.sf.basedb.core.Experiment

Get the publication text.

getPublicationDate() - Method in class net.sf.basedb.core.data.ExperimentData

Get the publication date for this experiment.

getPublicationDate() - Method in class net.sf.basedb.core.Experiment

Get the date this experiment was published.

getPublicLocalHost() - Static method in class net.sf.basedb.util.SocketUtil

Get the external address of the local host.

getPubMedId() - Method in class net.sf.basedb.core.data.ExperimentData

Get the publication for this experiment.

getPubMedId() - Method in class net.sf.basedb.core.Experiment

Get the PubMed ID of the publication.

getPushAnnotations() - Method in class net.sf.basedb.core.data.ItemSubtypeData

If this flag is set, the annotations on items of this subtype should be enabled for pushing to the parent item.

getPushAnnotations() - Method in class net.sf.basedb.core.ItemSubtype

If this flag is set, the annotations on items of this subtype can be pushed to the parent item.

getQualifiedTableName() - Method in class net.sf.basedb.core.RealTable

Get the quoted table name of this table in the database.

getQualifiedTableName(VirtualDb) - Method in enum class net.sf.basedb.core.VirtualTable

Get the real table name of this table in the database, quoted and with catalog/schema information prepended to it.

getQuantity() - Method in class net.sf.basedb.core.AnnotationType

Get the quantity for this annotation type.

getQuantity() - Method in class net.sf.basedb.core.data.AnnotationTypeData

Get the quantity this annotation type uses.

getQuantity() - Method in class net.sf.basedb.core.data.UnitData

Get the quantity this unit belongs to.

getQuantity() - Method in class net.sf.basedb.core.data.UnitSymbolData

Get the quantity this symbol belongs to.

getQuantity() - Method in class net.sf.basedb.core.Unit

Get the quantity this unit belongs to.

getQuery - Variable in enum class net.sf.basedb.core.Item

getQuery() - Static method in class net.sf.basedb.core.Annotation

Get a query configured to retrieve annotations.

getQuery() - Static method in class net.sf.basedb.core.AnnotationSet

Get a ItemQuery object configured to retrieve AnnotationSet items.

getQuery() - Static method in class net.sf.basedb.core.AnnotationTypeCategory

Get a ItemQuery object configured to retrieve AnnotationTypeCategory items.

getQuery() - Static method in class net.sf.basedb.core.ArrayBatch

Get a ItemQuery that returns array batches.

getQuery() - Static method in class net.sf.basedb.core.ArrayDesign

Get a ItemQuery object configured to retrieve array designs.

getQuery() - Static method in class net.sf.basedb.core.ArraySlide

Get a ItemQuery object configured to retrieve array slides.

getQuery() - Static method in class net.sf.basedb.core.BioPlate

Gets query that selects all available bioplates

getQuery() - Static method in class net.sf.basedb.core.BioPlateEvent

Get a query that returns bioplate event items.

getQuery() - Static method in class net.sf.basedb.core.BioPlateEventType

Gets query that returns bioplate event types.

getQuery() - Static method in class net.sf.basedb.core.BioPlateType

Gets query that selects all available bioplates

getQuery() - Static method in class net.sf.basedb.core.BioSource

Get a query that returns biosource items.

getQuery() - Static method in class net.sf.basedb.core.Client

Get a new query object for this class.

getQuery() - Static method in class net.sf.basedb.core.DataFileType

Get a query configured to retrieve DataFileType items.

getQuery() - Static method in class net.sf.basedb.core.DerivedBioAssay

Get a query that returns derived bioassay.

getQuery() - Static method in class net.sf.basedb.core.Directory

Get a query configured to retrieve directories.

getQuery() - Static method in class net.sf.basedb.core.Experiment

Get a query configured to retrieve experiments

getQuery() - Static method in class net.sf.basedb.core.Extract

Get a query that returns extracts.

getQuery() - Static method in class net.sf.basedb.core.ExtraValueType

Get a query configured to retrieve extra value types.

getQuery() - Static method in class net.sf.basedb.core.File

Get a query configured to retrieve File items.

getQuery() - Static method in class net.sf.basedb.core.FileServer

Get a new query object for this class.

getQuery() - Static method in class net.sf.basedb.core.FileSet

Get a ItemQuery object configured to retrieve FileSet items.

getQuery() - Static method in class net.sf.basedb.core.Formula

Get a new query object for this class.

getQuery() - Static method in class net.sf.basedb.core.GlobalDefaultSetting

Get a query configured to retrieve global default settings.

getQuery() - Static method in class net.sf.basedb.core.Group

Get a query configured to retrieve groups.

getQuery() - Static method in class net.sf.basedb.core.Hardware

Get a query configured to retrieve hardware.

getQuery() - Method in enum class net.sf.basedb.core.Item

Get a query returning items of this type.

getQuery() - Method in class net.sf.basedb.core.ItemContext

getQuery() - Static method in class net.sf.basedb.core.ItemList

Get a query that returns item lists.

getQuery() - Static method in class net.sf.basedb.core.Job

Get a query configured to retrieve jobs.

getQuery() - Static method in class net.sf.basedb.core.JobAgent

Get an ItemQuery that returns job agents.

getQuery() - Static method in class net.sf.basedb.core.Kit

Get a query configured to retrieve kits.

getQuery() - Static method in class net.sf.basedb.core.MimeType

Get a query configured to retrieve MIME types.

getQuery() - Static method in class net.sf.basedb.core.News

Get a query configured to retrieve news.

getQuery() - Static method in class net.sf.basedb.core.PermissionTemplate

Get a query that returns permission templates.

getQuery() - Static method in class net.sf.basedb.core.PhysicalBioAssay

Get a query that returns physical bioassays.

getQuery() - Static method in class net.sf.basedb.core.Plate

Get a query that returns plates.

getQuery() - Static method in class net.sf.basedb.core.PlateGeometry

Get a query configured to retrieve plate geometries.

getQuery() - Static method in class net.sf.basedb.core.PlateMapping

Get a query that returns plate mappings.

getQuery() - Static method in class net.sf.basedb.core.PlateType

Get a query that returns plate types.

getQuery() - Static method in class net.sf.basedb.core.Platform

Get a query configured to retrieve Platform items.

getQuery() - Static method in class net.sf.basedb.core.PlatformVariant

Get a query configured to retrieve PlatformVariant items.

getQuery() - Static method in class net.sf.basedb.core.PluginConfiguration

Get a query configured to retrieve plugin configurations.

getQuery() - Static method in class net.sf.basedb.core.PluginDefinition

Get a query that returns plugin definitions.

getQuery() - Static method in class net.sf.basedb.core.PluginType

Get a query configured to retrieve plugin types.

getQuery() - Static method in class net.sf.basedb.core.Project

Get a query configured to retrieve projects.

getQuery() - Static method in class net.sf.basedb.core.Protocol

Get a query configured to retrieve protocols.

getQuery() - Static method in class net.sf.basedb.core.Quantity

Get a query configured to retrieve quantities.

getQuery() - Static method in class net.sf.basedb.core.Quota

Get a query configured to retrieve quota.

getQuery() - Static method in class net.sf.basedb.core.QuotaType

Get a query configured to retrieve QuotaType.

getQuery() - Static method in class net.sf.basedb.core.RawBioAssay

Get a query configured to retrieve raw bioassays.

getQuery() - Static method in class net.sf.basedb.core.Reporter

Get a query object configured to retrieve reporters.

getQuery() - Static method in class net.sf.basedb.core.ReporterCloneTemplate

Get a query that returns reporter clone templates.

getQuery() - Static method in class net.sf.basedb.core.ReporterList

Get a new query object for this class.

getQuery() - Static method in class net.sf.basedb.core.ReporterType

Get a query configured to retrieve reporter types.

getQuery() - Static method in class net.sf.basedb.core.Role

Get a ItemQuery object configured to retrieve Role items.

getQuery() - Static method in class net.sf.basedb.core.RoleKey

Get a query object configured to retrieve role keys.

getQuery() - Static method in class net.sf.basedb.core.RootRawBioAssay

Get a query configured to retrieve raw bioassays.

getQuery() - Static method in class net.sf.basedb.core.Sample

Get a query that returns samples.

getQuery() - Static method in class net.sf.basedb.core.Software

Get a query configured to retrieve software.

getQuery() - Static method in class net.sf.basedb.core.Tag

Get a query that returns tags.

getQuery() - Static method in class net.sf.basedb.core.Unit

Get a query configured to retrieve units.

getQuery() - Static method in class net.sf.basedb.core.User

Get a query configured to retrieve users.

getQuery(Collection<RawBioAssay>) - Static method in class net.sf.basedb.core.DynamicRawDataQuery

Create a new dynamic query for raw data.

getQuery(ArrayDesign) - Static method in class net.sf.basedb.core.ArrayDesignBlock

Get a query configured to retrieve array design blocks for the specified array design.

getQuery(ArrayDesign) - Static method in class net.sf.basedb.core.ArrayDesignPlate

Get a query that returns ArrayDesignPlates connections for the specified array design.

getQuery(BioAssaySet) - Static method in class net.sf.basedb.core.BioAssay

Get a query configured to retrieve bioassays in a given bioassayset.

getQuery(BioAssaySet) - Static method in class net.sf.basedb.core.ExtraValue

Get a query configured to retrieve extra values in a given bioassayset.

getQuery(BioAssaySet) - Static method in class net.sf.basedb.core.Transformation

Get a query configured to retrieve transformations using the given bioassayset as source.

getQuery(BioMaterial) - Static method in class net.sf.basedb.core.BioMaterialEventSource

Get a query returning event information where a given biomaterial has been used as a source.

getQuery(BioMaterialEvent) - Static method in class net.sf.basedb.core.BioMaterialEventSource

Get a query returning source information for a given (creation) event.

getQuery(BioPlate) - Static method in class net.sf.basedb.core.BioPlateEventParticipant

Get a query configured to return all event participants for a bioplate.

getQuery(BioPlate) - Static method in class net.sf.basedb.core.BioWell

Get a query configured to retrieve wells for a plate.

getQuery(BioPlateEvent) - Static method in class net.sf.basedb.core.BioPlateEventParticipant

Get a query configured to return all participants for a bioplate event.

getQuery(Client) - Static method in class net.sf.basedb.core.ClientDefaultSetting

Get a query object configured to retrieve default settings for the specified client application.

getQuery(Client) - Static method in class net.sf.basedb.core.Help

Get a query configured to retrieve help texts for the specified client application.

getQuery(DataFileType) - Static method in class net.sf.basedb.core.ItemSubtypeFileType

Get the item subtype types that have been registered for a specific data file type.

getQuery(Experiment) - Static method in class net.sf.basedb.core.BioAssaySet

Get a query configured to retrieve bioassaysets for a given experiment.

getQuery(Experiment) - Static method in class net.sf.basedb.core.Transformation

Get a query configured to retrieve transformations for a given experiment.

getQuery(FileSet) - Static method in class net.sf.basedb.core.FileSetMember

Get a query configured to retrieve FileSetMember items.

getQuery(FileStoreEnabled) - Static method in class net.sf.basedb.core.DataFileType

Get a query configured to retrieve DataFileType:s that can be used on a given item.

getQuery(Formula.Type, RawDataType, IntensityTransform) - Static method in class net.sf.basedb.core.Formula

Get a query that return formulas that can be used with the specified raw data type.

getQuery(Item) - Static method in class net.sf.basedb.core.AnnotationType

Get a ItemQuery that returns annotation types.

getQuery(Item) - Static method in class net.sf.basedb.core.ItemSubtype

Get a query configured to retrieve item types.

getQuery(ItemList) - Static method in class net.sf.basedb.core.SyncFilter

Get a query configured to retrieve sync filters for the specified item list.

getQuery(ItemSubtype) - Static method in class net.sf.basedb.core.ItemSubtypeFileType

Get the file types that have been registered for a specific item subtype.

getQuery(JobAgent) - Static method in class net.sf.basedb.core.JobAgentSettings

Get a query configured to retrieve settings for the specified agent.

getQuery(MeasuredBioMaterial) - Static method in class net.sf.basedb.core.BioMaterialEvent

Get a query that returns events for a biomaterial.

getQuery(Plate) - Static method in class net.sf.basedb.core.PlateEvent

Get a query configured to retrieve plate events for the specified plate.

getQuery(Plate) - Static method in class net.sf.basedb.core.Well

Get a query configured to retrieve wells for a plate.

getQuery(PlateType) - Static method in class net.sf.basedb.core.PlateEventType

Get a query configured to retrieve event types for the specified plate type

getQuery(Platform, PlatformVariant, boolean) - Static method in class net.sf.basedb.core.PlatformFileType

Get the file types that have been registered for a specific platform and variant.

getQuery(Platform, PlatformVariant, Item, ItemSubtype) - Static method in class net.sf.basedb.core.DataFileType

Get a query to retrieve DataFileType:s that can be used on specific platform/variant for a given item and/or generic file type.

getQuery(GuiContext, String) - Static method in class net.sf.basedb.core.PluginConfiguration

Get a query that returns all plugins configurations related to a specified GUI context and implementing a certain interface.

getQuery(GuiContext, String) - Static method in class net.sf.basedb.core.PluginDefinition

Get a query that returns all plugins related to a specified GUI context and implementing a certain interface.

getQuery(PluginDefinition) - Static method in class net.sf.basedb.core.JobAgentSettings

Get a query configured to retrieve settings for the specified plugin.

getQuery(RawBioAssay) - Static method in class net.sf.basedb.core.DynamicRawDataQuery

Create a new dynamic query for raw data.

getQuery(ReporterList) - Static method in class net.sf.basedb.core.ReporterScore

Get a query object configured to retrieve reporters.

getQuery(Transformation) - Static method in class net.sf.basedb.core.BioAssaySet

Get a query configured to retrieve bioassaysets created by a given transformation.

getQuery(User) - Static method in class net.sf.basedb.core.Message

Get a query configured to retrieve messages for the specified user.

getQuery(User) - Static method in class net.sf.basedb.core.Session

Get a query configured to retrieve sessions for the specified user.

getQuery(User) - Static method in class net.sf.basedb.core.UserDefaultSetting

Get a query configured to retrieve default settings for a user.

getQuery(User) - Static method in class net.sf.basedb.core.UserDevice

Get a query configured to retrieve devices for the specified user.

getQuery(User, Client) - Static method in class net.sf.basedb.core.UserClientSetting

Get a query configured to retrieve client specific settings for a user.

getQuery(User, Group) - Static method in class net.sf.basedb.core.DiskUsage

Get a query configured to retrieve disk usage for the specified user.

getQueryClass() - Method in class net.sf.basedb.core.DynamicPositionQueryJoiners.ExtraValueJoiner

getQueryClass() - Method in class net.sf.basedb.core.DynamicPositionQueryJoiners.ReporterJoiner

getQueryClass() - Method in class net.sf.basedb.core.DynamicPositionQueryJoiners.ReporterListJoiner

getQueryClass() - Method in class net.sf.basedb.core.DynamicRawDataQuery.RawBioAssayJoiner

getQueryClass() - Method in class net.sf.basedb.core.DynamicRawDataQuery.ReporterJoiner

getQueryClass() - Method in class net.sf.basedb.core.DynamicRawDataQuery.ReporterListJoiner

getQueryClass() - Method in class net.sf.basedb.core.DynamicReporterQuery.MasterReporterJoiner

getQueryClass() - Method in class net.sf.basedb.core.DynamicReporterQuery.ReporterListJoiner

getQueryClass() - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.ExtraValueJoiner

getQueryClass() - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.RawDataJoiner

getQueryClass() - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.ReporterJoiner

getQueryClass() - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.ReporterListJoiner

getQueryClass() - Method in class net.sf.basedb.core.HqlQueryJoiners.AnnotationJoiner

getQueryClass() - Method in class net.sf.basedb.core.HqlQueryJoiners.ReporterListJoiner

getQueryClass() - Method in interface net.sf.basedb.core.query.AutoJoiner

The type of the query the implementation works for.

getQueryFile() - Static method in class net.sf.basedb.core.Application

Get the path to the XML file containing predefined queries for SQL and HQL.

getQueryOptions() - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

getQueryParameter(String) - Method in class net.sf.basedb.core.AbstractQuery

getQueryParameter(String) - Method in interface net.sf.basedb.core.query.Query

Get parameter information for the parameter with given name.

getQueryPropertyInspector() - Method in class net.sf.basedb.core.VirtualDb

Return a filter that can be used to check that a query is only using cloned reporter properties for sorting, filtering, etc.

getQueryRestriction() - Method in interface net.sf.basedb.core.query.QueryFilterAction

Generate a restriction for the entire query after all column and row filters has been processed.

getQueryReturns() - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

Deprecated.

getQuerySection() - Method in class net.sf.basedb.core.AbstractQuery

getQuerySection() - Method in interface net.sf.basedb.core.query.Query

Get the current section of the query that is beeing built.

getQueryString() - Method in class net.sf.basedb.core.hibernate.QueryWrapper

getQueryString(String, String...) - Static method in class net.sf.basedb.core.PredefinedQuery

Get the query string for the predefined query with the specified name.

getQueryType() - Method in class net.sf.basedb.core.AbstractEntityQuery

getQueryType() - Method in class net.sf.basedb.core.AbstractHqlQuery

getQueryType() - Method in class net.sf.basedb.core.AbstractSqlQuery

getQueryType() - Method in interface net.sf.basedb.core.query.Query

Get the type of query.

getQuota() - Method in class net.sf.basedb.core.data.GroupData

Get the quota object which holds quota information for this group.

getQuota() - Method in class net.sf.basedb.core.data.UserData

Get the quota object which holds quota information for this user.

getQuota() - Method in class net.sf.basedb.core.Group

Get the Quota that applies to the group.

getQuota() - Method in class net.sf.basedb.core.User

Get the Quota that applies to the user.

getQuotaGroup() - Method in class net.sf.basedb.core.data.UserData

Get the group this user is sharing quota with, or null if this user only has it's own quota.

getQuotaGroup() - Method in class net.sf.basedb.core.User

Get the Group whose Quota also applies to the user.

getQuotaType() - Method in class net.sf.basedb.core.data.DiskUsageData

Get the QuotaTypeData for this DiskUsageData.

getQuotaType() - Method in class net.sf.basedb.core.data.QuotaIndex

getQuotaType() - Method in class net.sf.basedb.core.DiskUsage

Get the QuotaType the DiskConsumable item is using.

getQuotaTypes() - Method in class net.sf.basedb.core.DiskUsageStatistics

Get the list of quota types that are registered for DiskConsumable items.

getQuotaTypeSystemId() - Method in interface net.sf.basedb.core.DiskConsumable

Get the QuotaType system id of this item.

getQuotaTypeSystemId() - Method in class net.sf.basedb.core.Experiment

Always QuotaType.EXPERIMENT.

getQuotaTypeSystemId() - Method in class net.sf.basedb.core.File

Always QuotaType.FILE.

getQuotaTypeSystemId() - Method in class net.sf.basedb.core.RawBioAssay

Always QuotaType.RAW_DATA.

getQuotaValue(QuotaType, Location) - Method in class net.sf.basedb.core.Quota

Get the quota for the specified type and location.

getQuotaValues() - Method in class net.sf.basedb.core.data.QuotaData

getQuotedName(String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine

Put quotes (") around the name.

getQuotedName(String) - Method in interface net.sf.basedb.core.dbengine.DbEngine

Quote the name with the database specific quote character.

getQuotedName(String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine

Put quotes (`) around the name.

getRawBioAssay() - Method in class net.sf.basedb.core.data.RawData

The raw bioassay this raw data spot belongs to.

getRawBioAssay() - Method in class net.sf.basedb.core.data.RootRawBioAssayData

Get the raw bioassay root raw bioassay is derived from.

getRawBioAssay() - Method in class net.sf.basedb.core.DynamicRawDataQuery

getRawBioAssay() - Method in class net.sf.basedb.core.RawDataBatcher

Get the raw bioassay this batcher is used for.

getRawBioAssay() - Method in class net.sf.basedb.core.RootRawBioAssay

Get the raw bioassay this root raw bioassay is representing.

getRawBioAssay(DbControl, RawData) - Static method in class net.sf.basedb.core.RawDataUtil

Get the raw bioassay the raw data belongs to.

getRawBioAssayData - Static variable in class net.sf.basedb.core.RawDataUtil

Method for calling RawData.getRawBioAssay()

getRawBioAssayQuery(Experiment) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter

Get a query that returns all raw bioassays which it may be possible to import raw data to for the given experiment.

getRawBioAssays() - Method in class net.sf.basedb.core.BioAssay

getRawBioAssays() - Method in class net.sf.basedb.core.data.DerivedBioAssayData

This is the inverse end.

getRawBioAssays() - Method in class net.sf.basedb.core.data.ExperimentData

Duplicates the mapping ExperimentData.getRootRawBioAssays().

getRawBioAssays() - Method in class net.sf.basedb.core.data.ExtractData

This is the inverse end.

getRawBioAssays() - Method in class net.sf.basedb.core.data.JobData

This is the inverse end.

getRawBioAssays() - Method in class net.sf.basedb.core.DerivedBioAssay

getRawBioAssays() - Method in class net.sf.basedb.core.Experiment

Get a query that returns the raw bioassays used in this experiment.

getRawBioAssays() - Method in class net.sf.basedb.core.Extract

Get a query that returns all raw bioassays created from this extract.

getRawData() - Method in class net.sf.basedb.core.RawBioAssay

Get a query that returns the raw data of this raw bioassay.

getRawData() - Method in class net.sf.basedb.util.jep.MeanFunction

Get the current raw data object used when evaluating the JEP expression.

getRawData() - Method in class net.sf.basedb.util.jep.RawFunction

Get the current raw data object used when evaluating the JEP expression.

getRawDataBatcher(FeatureIdentificationMethod, Job) - Method in class net.sf.basedb.core.RawBioAssay

Get a raw data batcher object which can be used to add raw data to the raw bioassay.

getRawDataById(int) - Method in class net.sf.basedb.core.RawBioAssay

Get a raw data spot when you know the id.

getRawDataById(int, boolean) - Method in class net.sf.basedb.core.RawBioAssay

Get a raw data spot when you know the id.

getRawDataById(DbControl, int) - Method in class net.sf.basedb.core.RawDataType

getRawdataFields(BioAssaySet) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin

getRawdataFields(BioAssaySet) - Method in class net.sf.basedb.plugins.BfsExporterPlugin

getRawDataJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicSpotQueryJoiners

Get a joiner instance for raw data for the specified join type.

getRawDataProperty(String, String) - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter

Find an extended raw data property with the given name and create a dynamic field from it using exportTitle as the title.

getRawDataType() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

getRawDataType() - Method in class net.sf.basedb.core.BioAssay

Get the raw data type the experiment uses for the raw data.

getRawDataType() - Method in class net.sf.basedb.core.BioAssaySet

Get the raw data type this experiment uses for the raw data.

getRawDataType() - Method in class net.sf.basedb.core.data.ExperimentData

Get the name of the raw data type used in this experiment.

getRawDataType() - Method in class net.sf.basedb.core.data.FormulaData

The name of raw data type this formula can be used on, or null if it can be used on any raw data type.

getRawDataType() - Method in class net.sf.basedb.core.data.ItemListData

Get the raw data type of raw bioassays that can be members in this list.

getRawDataType() - Method in class net.sf.basedb.core.data.PlatformData

The raw data type this platform is locked to, or null.

getRawDataType() - Method in class net.sf.basedb.core.data.PlatformVariantData

The raw data type this platform variant is locked to, or null.

getRawDataType() - Method in class net.sf.basedb.core.data.RawBioAssayData

Get the name of the raw data type used by this raw bio assay.

getRawDataType() - Method in class net.sf.basedb.core.DataCube

Get the raw data type this experiment uses for the raw data.

getRawDataType() - Method in class net.sf.basedb.core.DynamicRawDataQuery

getRawDataType() - Method in class net.sf.basedb.core.Experiment

Get the raw data type this experiment uses for the raw data.

getRawDataType() - Method in class net.sf.basedb.core.ExtraValue

Get the raw data type the experiment uses for the raw data.

getRawDataType() - Method in class net.sf.basedb.core.Formula

Get the raw data type this formula can be used on.

getRawDataType() - Method in class net.sf.basedb.core.ItemList

Get the raw data type of raw bioassays that can be members in this list.

getRawDataType() - Method in class net.sf.basedb.core.Platform

Get the raw data type this platform is locked to.

getRawDataType() - Method in class net.sf.basedb.core.PlatformVariant

Get the raw data type this platform variant is locked to.

getRawDataType() - Method in class net.sf.basedb.core.RawBioAssay

Get the raw data type this raw bioassay uses for the raw data.

getRawDataType() - Method in class net.sf.basedb.core.VirtualDb

Get the raw data type the experiment uses for the raw data.

getRawDataType() - Method in class net.sf.basedb.util.jep.RawFunction

Get the raw data type this function uses.

getRawDataType(String) - Static method in class net.sf.basedb.core.RawDataTypes

Get a information about a raw data type.

getRawDataTypeFiles() - Static method in class net.sf.basedb.core.Application

Get the path to the XML file containing raw data type definitions.

getRawDataTypes() - Static method in class net.sf.basedb.core.RawDataTypes

Get a collection with all raw data types that has been defined.

getRawParents() - Method in class net.sf.basedb.core.data.BioAssayData

Get a set that manages the raw parent bioassays the data in this bioassay is based on.

getRawSources() - Method in class net.sf.basedb.core.data.TransformationData

Get the source raw bioassays for the transformation.

getRawSources() - Method in class net.sf.basedb.core.Transformation

Get a query that returns the raw bioassay sources used by this transformation.

getRealTable() - Method in class net.sf.basedb.core.RawDataType

getReceivedSignals() - Method in class net.sf.basedb.core.signal.DelegatingSignalHandler

Get the list of received signals.

getReceivedSignals() - Method in class net.sf.basedb.core.signal.EnhancedThreadSignalHandler

Get the list of received signals.

getReceivedSignals() - Method in class net.sf.basedb.core.signal.ProgressReporterSignalHandler

Get the list of received signals.

getReceiverId() - Method in class net.sf.basedb.core.signal.AbstractSignalReceiver

Get the receiver ID that was passed to the AbstractSignalReceiver.init(String) method.

getReceiverId() - Method in class net.sf.basedb.core.signal.AbstractSignalTransporter

Get the receiverId part of the signal URI.

getRecent() - Method in class net.sf.basedb.clients.web.taglib.Select

getRecent(String) - Method in class net.sf.basedb.core.ItemContext

Get all recently used values for the specified key.

getRecent(String, int) - Method in class net.sf.basedb.core.ItemContext

getRecent(DbControl, Item) - Method in class net.sf.basedb.core.ItemContext

Get all recently used items of the specified type.

getRecent(DbControl, Item, int) - Method in class net.sf.basedb.core.ItemContext

getRecent(DbControl, Item, String) - Method in class net.sf.basedb.core.ItemContext

Get all recently used items of the specified type in a given sublist.

getRecent(DbControl, Item, String, int) - Method in class net.sf.basedb.core.ItemContext

getRecent(DbControl, Item, ItemSubtype) - Method in class net.sf.basedb.core.ItemContext

Get all recently used items of the specified type.

getRecentSettingName(String) - Method in class net.sf.basedb.core.ItemContext

getRedefinedColumnName(String, String) - Method in class net.sf.basedb.util.basefile.BaseFileParser

Get the redefined column name for a section.

getRefColumns() - Method in class net.sf.basedb.core.dbengine.TableInfo.ForeignKeyInfo

getReference(Class<T>, Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

getReferenceFactor() - Method in class net.sf.basedb.core.data.UnitData

Factor that controls how this unit relates to the reference unit of the quantity.

getReferenceFactor() - Method in class net.sf.basedb.core.Unit

Get the factor that is used for converting values in this unit into the reference unit of the quantity.

getReferenceOffset() - Method in class net.sf.basedb.core.data.UnitData

An offset that controls how this unit relates to the reference unit of the quantity.

getReferenceOffset() - Method in class net.sf.basedb.core.Unit

Get the offset that is used for converting values in this unit into the reference unit of the quantity.

getReferenceUnit() - Method in class net.sf.basedb.core.data.QuantityData

The reference unit that all units of must relate to.

getReferenceUnit() - Method in class net.sf.basedb.core.Quantity

The reference unit describes the unit that all other units must relate to.

getRefName() - Method in class net.sf.basedb.core.dbengine.TableInfo.ForeignKeyInfo

getRegion() - Method in class net.sf.basedb.util.GeoLocation

getRegistry() - Method in class net.sf.basedb.util.extensions.ExtensionContext

getRegistry() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext

getRegistry() - Method in class net.sf.basedb.util.extensions.InvokationContext

Get the registry where this invokation originated from.

getRegistry() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager

Get the registry in which all extensions that are managed by this manager are stored.

getRegistryBuilder() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration

Get the registry for collecting configuration options.

getRelatedItems(Annotatable, SourceItemTransformer) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn

Get all parent or child items to the requested item that matches the specified filter.

getRelatedItems(Item) - Static method in class net.sf.basedb.core.ItemSubtype

Get a list with (subtypable) items that are related to the given item (which should also be subtypable).

getRelatedSubtype(DbControl, Subtypable, Item...) - Static method in class net.sf.basedb.core.ItemSubtype

Utility method for locating a subtype that is related to the subtype of a given item.

getRelatedSubtype(DbControl, Subtypable, Item, int) - Static method in class net.sf.basedb.core.ItemSubtype

Same as ItemSubtype.getRelatedSubtype(DbControl, Subtypable, Item, int, int) with the same id for the last two parameters.

getRelatedSubtype(DbControl, Subtypable, Item, int, int) - Static method in class net.sf.basedb.core.ItemSubtype

Utility method for loading a subtype that is related to the subtype of the given item.

getRelatedSubtype(Item) - Method in class net.sf.basedb.core.ItemSubtype

Get a related subtype of another item type.

getRelatedSubtypes() - Method in class net.sf.basedb.core.data.ItemSubtypeData

getRelatedSubtypes() - Method in class net.sf.basedb.core.ItemSubtype

Get a query returning all subtypes that are related to this subtype.

getRelativePath(File) - Static method in class net.sf.basedb.core.File

Get the relative path of the specified file from the base upload directory and convert directory separator to forward slash.

getReload() - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring

Never reload since everything is static.

getReload() - Method in class net.sf.basedb.core.Job.SignalKeyring

Never reload since everything is static.

getReload() - Method in class net.sf.basedb.core.Keyring

getReload() - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring

Never reload since everything is static.

getRemainingQuantity() - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData

Get the remaining quantity of the biomaterial.

getRemainingQuantity() - Method in class net.sf.basedb.core.MeasuredBioMaterial

Get the remaining quantity of the biomaterial.

getRemoteAddresses(String) - Method in class net.sf.basedb.clients.jobagent.Agent

Split the string at commas and try to create an InetAddress for each part.

getRemoteId() - Method in class net.sf.basedb.core.data.SessionData

Get the login comment.

getRemoteId() - Method in class net.sf.basedb.core.Session

Get the remote ID of the host the user used for this session.

getRemoteId() - Method in class net.sf.basedb.core.SessionControl

Get the remote id that was passed to the Application.newSessionControl(String,String,String) method when creating this object.

getRemoteSlot(String) - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager

Get the remote slot with the given id.

getRemoteSlot(Job.ExecutionTime) - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager

Create a slot for a job on a remote job agent with the specified estimated execution time.

getRemovableItems() - Static method in class net.sf.basedb.core.Metadata

Get a set containing all Removable item types.

getRemove() - Method in class net.sf.basedb.util.annotations.InheritSpecification

getRemovedBy() - Method in class net.sf.basedb.core.BioAssaySet

getRemovedBy() - Method in class net.sf.basedb.core.BioPlateEventType

getRemovedBy() - Method in class net.sf.basedb.core.BioPlateType

getRemovedBy() - Method in class net.sf.basedb.core.CommonItem

getRemovedBy() - Method in class net.sf.basedb.core.data.BioAssaySetData

getRemovedBy() - Method in class net.sf.basedb.core.data.BioPlateEventTypeData

getRemovedBy() - Method in class net.sf.basedb.core.data.BioPlateTypeData

getRemovedBy() - Method in class net.sf.basedb.core.data.CommonData

getRemovedBy() - Method in class net.sf.basedb.core.data.DataFileTypeData

getRemovedBy() - Method in class net.sf.basedb.core.data.ExtraValueTypeData

getRemovedBy() - Method in class net.sf.basedb.core.data.GroupData

getRemovedBy() - Method in class net.sf.basedb.core.data.ItemSubtypeData

getRemovedBy() - Method in class net.sf.basedb.core.data.MessageData

getRemovedBy() - Method in class net.sf.basedb.core.data.MimeTypeData

getRemovedBy() - Method in class net.sf.basedb.core.data.NewsData

getRemovedBy() - Method in class net.sf.basedb.core.data.PlateEventTypeData

getRemovedBy() - Method in class net.sf.basedb.core.data.PlateGeometryData

getRemovedBy() - Method in class net.sf.basedb.core.data.PlatformData

getRemovedBy() - Method in class net.sf.basedb.core.data.PlatformVariantData

getRemovedBy() - Method in class net.sf.basedb.core.data.PluginDefinitionData

getRemovedBy() - Method in class net.sf.basedb.core.data.PluginTypeData

getRemovedBy() - Method in class net.sf.basedb.core.data.ProjectData

getRemovedBy() - Method in class net.sf.basedb.core.data.QuantityData

getRemovedBy() - Method in class net.sf.basedb.core.data.QuotaData

getRemovedBy() - Method in interface net.sf.basedb.core.data.RemovableData

Get the ID of the user that removed this item.

getRemovedBy() - Method in class net.sf.basedb.core.data.ReporterTypeData

getRemovedBy() - Method in class net.sf.basedb.core.data.RoleData

getRemovedBy() - Method in class net.sf.basedb.core.data.TransformationData

getRemovedBy() - Method in class net.sf.basedb.core.data.UnitData

getRemovedBy() - Method in class net.sf.basedb.core.data.UserData

getRemovedBy() - Method in class net.sf.basedb.core.DataFileType

getRemovedBy() - Method in class net.sf.basedb.core.Directory

getRemovedBy() - Method in class net.sf.basedb.core.ExtraValueType

getRemovedBy() - Method in class net.sf.basedb.core.Group

getRemovedBy() - Method in class net.sf.basedb.core.ItemSubtype

getRemovedBy() - Method in class net.sf.basedb.core.Message

getRemovedBy() - Method in class net.sf.basedb.core.MimeType

getRemovedBy() - Method in class net.sf.basedb.core.News

getRemovedBy() - Method in class net.sf.basedb.core.PlateEventType

getRemovedBy() - Method in class net.sf.basedb.core.PlateGeometry

getRemovedBy() - Method in class net.sf.basedb.core.Platform

getRemovedBy() - Method in class net.sf.basedb.core.PlatformVariant

getRemovedBy() - Method in class net.sf.basedb.core.PluginType

getRemovedBy() - Method in class net.sf.basedb.core.Project

getRemovedBy() - Method in class net.sf.basedb.core.Quantity

getRemovedBy() - Method in class net.sf.basedb.core.Quota

getRemovedBy() - Method in interface net.sf.basedb.core.Removable

Get the user that flagged this item for removal.

getRemovedBy() - Method in class net.sf.basedb.core.ReporterType

getRemovedBy() - Method in class net.sf.basedb.core.Role

getRemovedBy() - Method in class net.sf.basedb.core.Transformation

getRemovedBy() - Method in class net.sf.basedb.core.Unit

getRemovedBy() - Method in class net.sf.basedb.core.User

getRemoveJobWhenFinished() - Method in class net.sf.basedb.core.data.JobData

If the core should delete the job when it's finished successfully.

getRemoveJobWhenFinished() - Method in class net.sf.basedb.core.Job

If the job should flagged for deletion after it's done successfully.

getRenderer() - Method in class net.sf.basedb.util.extensions.ActionIterator

Gets the renderer for the current action.

getRenderer() - Method in class net.sf.basedb.util.extensions.ExtensionContext

If the extension point allows it and this extension specifies a renderer factory, create a new renderer from it.

getRenderer() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext

If the extension point defines a renderer factory, creates a new renderer unless one already exists.

getRenderer() - Method in class net.sf.basedb.util.extensions.InvokationContext

Get the renderer, if any.

getRenderer(InvokationContext<? extends A>) - Method in interface net.sf.basedb.util.extensions.RendererFactory

Get a renderer for a given context.

getRenderer(InvokationContext<? extends ButtonAction>) - Method in class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRendererFactory

getRenderer(InvokationContext<? extends ButtonAction>) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarButtonRendererFactory

getRendererFactory() - Method in interface net.sf.basedb.util.extensions.Extension

Get an optional factory class for creating renderers for the actions.

getRendererFactory() - Method in class net.sf.basedb.util.extensions.ExtensionBean

getRendererFactory() - Method in interface net.sf.basedb.util.extensions.ExtensionPoint

This is an optional factory for creating Renderer instances.

getRendererFactory() - Method in class net.sf.basedb.util.extensions.ExtensionPointBean

getRendererFactory() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension

getRendererFactory() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint

getReplaceExisting() - Method in class net.sf.basedb.util.annotations.InheritSpecification

getReporter() - Method in class net.sf.basedb.core.data.FeatureData

Get the reporter of the feature.

getReporter() - Method in class net.sf.basedb.core.data.RawData

The reporter this raw data is connected with.

getReporter() - Method in class net.sf.basedb.core.data.ReporterListScoreData

Get the reporter.

getReporter() - Method in class net.sf.basedb.core.data.WellData

The reporter used in this well.

getReporter() - Method in class net.sf.basedb.core.ReporterScore

Get the reporter.

getReporter() - Method in class net.sf.basedb.core.Well

Get the reporter in this well.

getReporter() - Method in class net.sf.basedb.util.jep.ReporterFunction

Get the current reporter object used when evaluating the JEP expression.

getReporter(boolean) - Method in class net.sf.basedb.core.Well

Get the reporter in this well.

getReporter(DbControl, int) - Method in class net.sf.basedb.clients.web.ExperimentExplorer

Get the reporter for the specified index.

getReporter(RawDataBatcher.ReporterProxy) - Method in class net.sf.basedb.core.RawDataBatcher.FeatureInfo

getReporterAnnotationsWriter() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter

Get the writer were reporter annotations should be printed.

getReporterCloneBatcher(DbControl) - Method in class net.sf.basedb.core.Experiment

Get a batcher for managing cloned reporter information for this experiment.

getReporterCloneTemplate() - Method in class net.sf.basedb.core.data.VirtualDbData

Get the template used for creating the cloned reporter table in this virtual database, or null if there is no cloned reporter information.

getReporterCloneTemplate() - Method in class net.sf.basedb.core.VirtualDb

Get the reporter clone template that is active in the current virtual database.

getReporterField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.AdvancedFieldConverter

getReporterField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.Base1FieldConverter

Convert a reporter field.

getReporterField(String, boolean) - Method in interface net.sf.basedb.util.export.spotdata.ExportableFieldConverter

Create a reporter dynamic field for the given name.

getReporterField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.StandardFieldConverter

Find a reporter dynamic field.

getReporterFields() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin

getReporterFields() - Static method in class net.sf.basedb.plugins.BfsExporterPlugin

getReporterFields() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

Get the list of registered reporter fields, in the order they were registered.

getReporterFields() - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter

getReporterFields() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter

getReporterId() - Method in class net.sf.basedb.core.data.ReporterListScoreData

The id of the reporter.

getReporterId(int) - Method in class net.sf.basedb.clients.web.ExperimentExplorer

Get the reporter id for the specified index.

getReporterIndex() - Method in class net.sf.basedb.clients.web.ExperimentExplorer

Get the index of the current reporter.

getReporterJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicPositionQueryJoiners

Get a joiner instance for reporters for the specified join type.

getReporterJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicSpotQueryJoiners

Get a joiner instance for reporters for the specified join type.

getReporterList() - Method in class net.sf.basedb.core.data.ReporterListScoreData

The reporter list this reporter and score belongs to.

getReporterList() - Method in class net.sf.basedb.core.query.ReporterListExpression

Get the reporter list.

getReporterListJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicPositionQueryJoiners

Get a joiner instance for reporter lists for the specified join type.

getReporterListJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicReporterQuery

Get a joiner instance for reporter lists for the specified join type.

getReporterListJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicSpotQueryJoiners

Get a joiner instance for raw data for the specified join type.

getReporterListJoiner(JoinType) - Static method in class net.sf.basedb.core.HqlQueryJoiners

Get a joiner instance for raw data for the specified join type.

getReporterLists() - Method in class net.sf.basedb.core.data.ExperimentData

This is the inverse end.

getReporterListScores() - Method in class net.sf.basedb.core.data.ReporterData

The lists this reporter is used in.

getReporterListScores() - Method in class net.sf.basedb.core.data.ReporterListData

The list of reporters and their scores.

getReporterListsEnum(DbControl) - Static method in class net.sf.basedb.clients.web.Base

getReporterProperty(String, String) - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter

Get a static or extended reporter property field, such as name, description or id.

getReporterQuery() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

Get a configured query for position data that returns all fields that has been registered with AbstractBioAssaySetExporter.addReporterField(DynamicField).

getReporterQuery(DbControl, List<String>) - Method in class net.sf.basedb.clients.web.ExperimentExplorer

Get a query returning the reporter data used by the reporter search page.

getReporters() - Method in class net.sf.basedb.core.ArrayDesign

Get a query that returns the reporters on this array design.

getReporters() - Method in class net.sf.basedb.core.data.ReporterTypeData

This is the inverse end.

getReporters() - Method in class net.sf.basedb.core.Plate

Get a query that returns the reporters on this plate.

getReporters() - Method in class net.sf.basedb.core.RawBioAssay

Get a query that returns the reporters on this raw bioassay.

getReporterScores() - Method in class net.sf.basedb.core.ReporterList

Get a query returning ReporterScore objects.

getReporterType() - Method in class net.sf.basedb.core.data.ReporterData

Get the ReporterTypeData of this the reporter.

getReporterType(String) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter

getReporterType(DbControl, ReporterData) - Static method in class net.sf.basedb.core.Reporter

Get the reporter type item from a reporter data object.

getRequestInformation() - Method in class net.sf.basedb.core.PluginConfigurationRequest

Get the request information object containing information about the parameters needed for the plugin.

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.clients.web.plugins.SimpleExport

getRequestInformation(GuiContext, String) - Method in interface net.sf.basedb.core.plugin.InteractivePlugin

This method will return the RequestInformation for a given command, i.e.

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.Base1PluginExecuter

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.BfsExporterPlugin

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.CdfFileReporterImporter

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.executor.BaseFileExporterSupport

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.executor.BaseFileImporterSupport

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.executor.BfsExporterSupport

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.executor.BfsImporterSupport

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.FormulaFilter

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.GalExporter

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.HelpExporter

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.HelpImporter

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin

The Request.COMMAND_CONFIGURE_PLUGIN command will not ask for any parameters.

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.JepExtraValueCalculator

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.JepIntensityTransformer

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.LowessNormalization

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.ManualTransformCreator

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.MedianRatioNormalization

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.PackedFileExporter

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.PlateFlatFileImporter

The Request.COMMAND_CONFIGURE_PLUGIN command will ask for parser regular expressions and column mappings.

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.PlateMappingExporter

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.PlateMappingImporter

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.PluginConfigurationExporter

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.PluginConfigurationImporter

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter

The Request.COMMAND_CONFIGURE_PLUGIN command will ask for parser regular expressions and column mappings.

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter

The Request.COMMAND_CONFIGURE_PLUGIN command will ask for what type of rawdata to import.

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter

The Request.COMMAND_CONFIGURE_PLUGIN command will ask for parser regular expressions, column mappings and the reporter type.

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

The Request.COMMAND_CONFIGURE_PLUGIN command will ask for parser regular expressions and column mappings.

getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker

getRequiredFilter(Item) - Static method in class net.sf.basedb.core.QueryRuntimeFilterFactory

Get the required runtime filter for the speicified item type.

getRequiredHeader(FlatFileParser, String, String, String) - Method in class net.sf.basedb.util.basefile.BaseFileParser

Get the value of a required header.

getRequiredHeader(FlatFileParser, String, String, String, String) - Method in class net.sf.basedb.util.basefile.BaseFileParser

Get the value of a header as a list of sub-values.

getRequiredIndex(List<String>, String, String, String, int, String) - Method in class net.sf.basedb.util.basefile.BaseFileParser

Get the index of value in a list of values or throw an exception if the value is not found.

getRequiredString(String, String) - Static method in class net.sf.basedb.core.Config

Get a required configuration setting.

getRequiresConfiguration() - Method in class net.sf.basedb.core.data.PluginDefinitionData

If the plugin requires a configurations or not.

getResetClassLoader() - Method in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor

getResetrrorFlag() - Method in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor

getResource(String) - Method in class net.sf.basedb.util.JarClassLoader

getResourceBundle() - Method in class net.sf.basedb.util.resources.ResourceBundleWrapper

Get access to the underlying resource bundle.

getResourceBundle(String, Locale) - Static method in class net.sf.basedb.util.resources.ResourceBundleFactory

Same as getResouceBundle(name, locale, null).

getResourceBundle(String, Locale, ClassLoader) - Static method in class net.sf.basedb.util.resources.ResourceBundleFactory

Get a resource bundle for the given locale.

getResourceBundle(String, SessionControl) - Static method in class net.sf.basedb.util.resources.ResourceBundleFactory

Same as getResouceBundle(name, sc, null).

getResourceBundle(String, SessionControl, ClassLoader) - Static method in class net.sf.basedb.util.resources.ResourceBundleFactory

Get a resource bundle for the given session control.

getResources(String) - Method in class net.sf.basedb.util.JarClassLoader

getResponseImpl() - Method in class net.sf.basedb.core.PluginResponse

Get a new reponse object.

getRestriction() - Method in class net.sf.basedb.core.ItemContext.QueryRestrictions

getRestriction(DbControl, EntityQuery) - Method in class net.sf.basedb.core.PropertyFilter

Create a restriction from the filter.

getRestriction(DbControl, EntityQuery, ClientContext) - Method in class net.sf.basedb.core.PropertyFilter

Create a restriction from the filter.

getRestriction(Expression, Expression) - Method in enum class net.sf.basedb.core.Operator

getRestriction(Expression, Expression[]) - Method in enum class net.sf.basedb.core.Operator

getRestrictionSql(Query, DbControl) - Method in class net.sf.basedb.core.AnnotationBetweenRestriction

getRestrictionSql(Query, DbControl) - Method in class net.sf.basedb.core.AnnotationInRestriction

getRestrictionSql(Query, DbControl) - Method in class net.sf.basedb.core.AnnotationRestriction

Get an SQL fragment that includes the actual restriction.

getRestrictionSql(Query, DbControl) - Method in class net.sf.basedb.core.AnnotationSimpleRestriction

getRestrictionSql(Query, DbControl) - Method in class net.sf.basedb.core.HasAnnotationRestriction

getResult(ResultSet) - Method in class net.sf.basedb.core.AbstractSqlQuery.CountWork

getResult(ResultSet) - Method in class net.sf.basedb.core.hibernate.ResultSetWork

This method needs to be overridden by subclasses to extract the result from the ResultSet.

getResultIntensityTransform() - Method in class net.sf.basedb.core.data.FormulaData

A flag indicating what kind of result spot data this formula generates, or null if it generates the same kind of data that is used as source. 0 = no transformation; 1 = 2-log; 2 = 10-log

getResultIntensityTransform() - Method in class net.sf.basedb.core.Formula

Get the spot intensity transformation that this formula generates.

getResults(ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.ProcessResults

Get the results for a specific extensions file.

getResync() - Method in class net.sf.basedb.util.annotations.InheritSpecification

getReturnAliases() - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

getReturnType() - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter

Always return null.

getReturnTypes() - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

getReverseDirection() - Method in enum class net.sf.basedb.core.ItemContext.SortDirection

Get the reverse sort direction.

getRole() - Method in class net.sf.basedb.core.BioPlateEventParticipant

Get the role that the plate has in this event.

getRole() - Method in class net.sf.basedb.core.data.BioPlateEventParticipantData

Get the role of the plate in the event.

getRoleId() - Method in class net.sf.basedb.core.data.keyring.RoleKeys

Get the id of the role.

getRoleId() - Method in class net.sf.basedb.core.data.keyring.UserRoles

Get the id of the role.

getRoleKeyId(Item) - Static method in class net.sf.basedb.core.SystemItems

Get the numeric id for a RoleKey when you know the Item type of the RoleKey.

getRolePermissions(Item) - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring

Return Permission.ACT_AS_ANOTHER_USER if itemType = Item.SYSTEM, 0 otherwise.

getRolePermissions(Item) - Method in class net.sf.basedb.core.Job.SignalKeyring

Return Permission.WRITE if itemType = Item.JOB, Permission.READ if Item.USER and Permission.CREATE if Item.MESSAGE or 0 otherwise.

getRolePermissions(Item) - Method in class net.sf.basedb.core.Keyring

Get the logged in user's permission to an unspecified item of a certain Item type.

getRolePermissions(Item) - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring

Return Permission.ACT_AS_ANOTHER_USER if itemType = Item.SYSTEM, 0 otherwise.

getRolePermissions(Item) - Method in class net.sf.basedb.core.SessionControl

Get all role-based permissions for the specified type of items.

getRoles() - Method in class net.sf.basedb.core.data.RoleKeyData

Get the map that manages which roles that have permissions for this key.

getRoles() - Method in class net.sf.basedb.core.data.UserData

This is the inverse end.

getRoles() - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring

Return empty set.

getRoles() - Method in class net.sf.basedb.core.Job.SignalKeyring

Return empty set.

getRoles() - Method in class net.sf.basedb.core.Keyring

getRoles() - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring

Return empty set.

getRoles() - Method in class net.sf.basedb.core.SessionControl

Deprecated.

In 3.11, use SessionControl.getAllRoles() or SessionControl.getActiveRoles() instead

getRoles() - Method in class net.sf.basedb.core.User

Get a query that returns the roles where this user is a member.

getRoot() - Method in class net.sf.basedb.clients.web.extensions.JspContext

Get the URL to the web application root as a string.

getRoot() - Method in class net.sf.basedb.clients.web.taglib.menu.Menu

getRoot() - Method in class net.sf.basedb.clients.web.taglib.Page

getRoot() - Method in class net.sf.basedb.clients.web.taglib.path.Path

getRoot() - Method in class net.sf.basedb.clients.web.taglib.PropertyValue

getRoot() - Method in class net.sf.basedb.util.extensions.xml.PathConverter

Get the value of the root path.

getRootAlias() - Method in class net.sf.basedb.core.AbstractHqlQuery

The alias of the item that is the root of this query.

getRootAlias() - Method in class net.sf.basedb.core.DynamicQuery

The alias of the item that is returned by this query.

getRootAlias() - Method in class net.sf.basedb.core.DynamicRawDataQuery

The alias of the item that is returned by this query.

getRootAlias() - Method in class net.sf.basedb.core.DynamicReporterQuery

The alias of the item that is returned by this query.

getRootAlias() - Method in interface net.sf.basedb.core.query.Query

The alias of the root-entity in the FROM part.

getRootDerivedBioAssays() - Method in class net.sf.basedb.core.data.PhysicalBioAssayData

This is the inverse end with an extra restriction

getRootDerivedBioAssays() - Method in class net.sf.basedb.core.PhysicalBioAssay

Get a query that returns all root derived bioassay created from this physical bioassay.

getRootEntry() - Method in class net.sf.basedb.util.Tree

Get the entry for the root node.

getRootItem() - Method in class net.sf.basedb.util.overview.GenericOverview

Get the root item of this overview.

getRootNode() - Method in class net.sf.basedb.util.overview.GenericOverview

Get the root node.

getRootPath() - Method in class net.sf.basedb.core.data.FileServerData

Get the root path that must be added to all URI:s using this file server.

getRootPath() - Method in class net.sf.basedb.core.FileServer

getRootPath() - Method in class net.sf.basedb.util.uri.ConnectionParameters

Get the root path that must be added to all URI:s used with these connection parameters.

getRootPath(DbControl) - Method in class net.sf.basedb.plugins.batchimport.FileImporter

getRootRawBioAssay(RawBioAssay) - Method in class net.sf.basedb.core.Experiment

Get the root raw bioassay that represents the given raw bioassay in this experiment.

getRootRawBioAssays() - Method in class net.sf.basedb.core.BioAssay

getRootRawBioAssays() - Method in class net.sf.basedb.core.data.ExperimentData

Manages which raw bioassays are available in the experiment.

getRootRawBioAssays() - Method in class net.sf.basedb.core.Experiment

Get a query that returns the root raw bioassays used in this experiment.

getRootTable() - Method in class net.sf.basedb.core.DynamicQuery

getRootTable() - Method in class net.sf.basedb.core.DynamicRawDataQuery

getRootTransformations() - Method in class net.sf.basedb.core.Experiment

Get a query that return all root transformations in this experiment.

getRootType() - Method in class net.sf.basedb.core.AbstractEntityQuery

getRootType() - Method in interface net.sf.basedb.core.query.EntityQuery

The type of items that is the root of the query.

getRow() - Method in class net.sf.basedb.clients.web.taglib.table.PropertyFilter

getRow() - Method in class net.sf.basedb.core.BioWell

Gets the row index where this well is located.

getRow() - Method in class net.sf.basedb.core.data.BioWellData

The row coordinate of this well.

getRow() - Method in class net.sf.basedb.core.data.FeatureData

Get the row coordinate of the feature.

getRow() - Method in class net.sf.basedb.core.data.MappingCoordinate

Get the row number.

getRow() - Method in class net.sf.basedb.core.data.PlateCoordinate

Get the row number.

getRow() - Method in class net.sf.basedb.core.data.RawData

getRow() - Method in class net.sf.basedb.core.data.WellData

The row coordinate of this well.

getRow() - Method in class net.sf.basedb.core.FeatureCoordinate

getRow() - Method in class net.sf.basedb.core.Well

Get the row coordinate of this well on the plate.

getRow(int) - Method in class net.sf.basedb.core.ItemContext.QueryRestrictions

getRowById(int) - Method in class net.sf.basedb.util.bfs.AnnotationModel

getRowByIndex(int) - Method in class net.sf.basedb.util.bfs.AnnotationModel

getRowByIndex(int) - Method in class net.sf.basedb.util.bfs.MatrixModel

getRowCount() - Method in class net.sf.basedb.util.bfs.AnnotationModel

Get the number of rows.

getRowCount() - Method in class net.sf.basedb.util.bfs.MatrixModel

Get the number of rows.

getRowCount(DbEngine, Connection, boolean) - Method in class net.sf.basedb.core.dbengine.TableInfo

Count the number of rows in the table.

getRowId(int) - Method in class net.sf.basedb.util.bfs.AnnotationModel

Get the row id for a given row.

getRowIndex() - Method in class net.sf.basedb.core.PropertyFilter

Get the filter row index this filter is part of.

getRowIndex(int) - Method in class net.sf.basedb.util.bfs.AnnotationModel

Get the row index for a given row id.

getRowRestriction() - Method in class net.sf.basedb.core.ItemContext.RowRestrictions

getRowRestriction(int) - Method in interface net.sf.basedb.core.query.QueryFilterAction

Generate a restriction for the given filter row.

getRows() - Method in class net.sf.basedb.core.BioPlate

Get the number of rows on this plate.

getRows() - Method in class net.sf.basedb.core.data.PlateGeometryData

The number of rows in this geometry.

getRows() - Method in class net.sf.basedb.core.PlateGeometry

Get the number of rows in this geometry.

getRowSelectionForLimitHandler() - Method in class net.sf.basedb.core.AbstractSqlQuery

Get a RowSelection object to be used with a LimitHandler so that it can modify and add parameters to the SQL.

getRowSeparator() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil

Get the current row separator.

getRowsperpage() - Method in class net.sf.basedb.clients.web.taglib.table.Navigator

getRowsPerPage() - Method in class net.sf.basedb.core.data.ContextData

Get the number of rows that are displayed on each table page.

getRowsPerPage() - Method in class net.sf.basedb.core.ItemContext

Get the number of rows the current table page is displaying.

getRunningJobs() - Method in class net.sf.basedb.clients.jobagent.Agent

Get a set containing the ID:s of the jobs that are currently beeing executed by this job agent.

getSafeRawDataType(String) - Static method in class net.sf.basedb.core.RawDataTypes

Get a information about a raw data type or throw an exception if the raw data type is not found.

getSameUnitsParameter() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport

getSamples() - Method in class net.sf.basedb.core.BioSource

Get a query that returns all samples created from this biosource.

getSampleSize() - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics

Get the number of items that was sampled to generated the statistics.

getSaveAsParameter(String, String, String, boolean) - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin

Get a plugin parameter that asks for the path to a file where the exported data should be saved.

getSaveAsPath(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin

Get the configured path where the exported data should be saved.

getSaveTo() - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin

Get the file object that the current export is writing to.

getSc() - Method in class net.sf.basedb.clients.web.taglib.table.Table

getScale(SessionControl) - Static method in class net.sf.basedb.clients.web.Base

Get the display scale setting.

getScheduled() - Method in class net.sf.basedb.core.data.JobData

Get the date and time the job was scheduled to the job queue, or null if it hasn't been scheduled yet.

getScheduled() - Method in class net.sf.basedb.core.Job

Get the date and time the job was scheduled to the job queue.

getScheduler() - Static method in class net.sf.basedb.core.Application

Get a scheduler that can be used for registering TimerTask for executions.

getSchema() - Method in class net.sf.basedb.core.hibernate.SessionFactoryConfiguration

Deprecated.

Get the schema.

getSchema() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration

Get the schema.

getSchemaName(String, String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine

Return the schema name.

getSchemaName(String, String) - Method in interface net.sf.basedb.core.dbengine.DbEngine

Get the schema name to use for referencing the given catalog/schema pair.

getSchemaName(String, String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine

Return null.

getSchemaValidatedXML(InputStream, String, String...) - Static method in class net.sf.basedb.util.XmlUtil2

Validate an XML input stream using XML schemas.

getSchemaValidatedXML(URL, String...) - Static method in class net.sf.basedb.util.XmlUtil2

Validate an XML file using XML schemas.

getSchemaVersion() - Static method in class net.sf.basedb.core.Application

Get the current database schema version number.

getSchemaVersion() - Method in class net.sf.basedb.core.data.SchemaVersionData

The current schema version.

getSchemaVersion() - Method in class net.sf.basedb.core.hibernate.SessionFactoryConfiguration

Deprecated.

Get the schema version of the current configuration.

getSchemaVersion() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration

Get the schema version of the current configuration.

getSchemaVersion(Session, String) - Static method in class net.sf.basedb.core.Update

getSchemaVersionInTransaction(Session, String) - Static method in class net.sf.basedb.core.Update

Get the current schema version number as it is stored in the database.

getScore() - Method in class net.sf.basedb.core.data.ReporterListScoreData

Get the score for the reporter, or null if no score has been set.

getScore() - Method in class net.sf.basedb.core.ReporterScore

Get the score for this reporter or null if no score has been set.

getScore() - Method in class net.sf.basedb.util.fuzzy.StringMatcher.FuzzyMatch

Get the similarity score of the key/value strings.

getScore(String, String) - Method in class net.sf.basedb.util.fuzzy.StringMatcher

Get the similarity score of two strings.

getScore(ReporterData) - Method in class net.sf.basedb.core.ReporterList

Get the score for the specified reporter.

getScripts() - Method in class net.sf.basedb.clients.web.extensions.AbstractJspFactory

Get a set with all script references.

getScripts() - Method in class net.sf.basedb.clients.web.extensions.JspContext

Get all scripts that has been added to this context.

getScripts() - Method in class net.sf.basedb.clients.web.taglib.Head

getScripts(String) - Method in class net.sf.basedb.clients.web.extensions.JspContext

Get all scripts that has been added to this context by the given extension

getScriptSourceInput() - Method in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget

getScriptTargetOutput() - Method in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget

getSection() - Method in class net.sf.basedb.core.BioPlate

Get the section within the "storage location" for this bioplate.

getSection() - Method in class net.sf.basedb.core.data.BioPlateData

Get the section in the storage location were the bioplate is stored.

getSection(int) - Method in class net.sf.basedb.util.bfs.MetadataModel

Get the section at a given index.

getSection(String) - Method in class net.sf.basedb.util.bfs.MetadataModel

Get the first section with a given name.

getSectionCount() - Method in class net.sf.basedb.util.bfs.MetadataModel

Get the number of sections.

getSectionCount() - Method in class net.sf.basedb.util.bfs.MetadataWriter

Get the number of sections that has been written to this file so far.

getSectionCount(String) - Method in class net.sf.basedb.util.basefile.BaseFileParser

The number of times we have seen a certain section in the file.

getSectionParser(String) - Method in class net.sf.basedb.util.basefile.BaseFileParser

Get the parser that is currently registered for a section.

getSelectdefault() - Method in class net.sf.basedb.clients.web.taglib.Select

getSelected() - Method in class net.sf.basedb.core.ItemContext

Get a Set object to specify the ID:s of all items that are currently selected.

getSelectedColumns(ItemContext, List<TableColumn>, boolean) - Static method in class net.sf.basedb.clients.web.DynamicUtil

getSelectrecent() - Method in class net.sf.basedb.clients.web.taglib.Select

getSelects() - Method in class net.sf.basedb.core.AbstractQuery

Get all non-permanent selects.

getSender() - Method in class net.sf.basedb.core.Message

Get the user that sent this message.

getSendMessage() - Method in class net.sf.basedb.core.data.JobData

If the core should send a message to the owner when the job is finished or not.

getSendMessage() - Method in class net.sf.basedb.core.Job

If a message should be sent to the owner once the job has finished or not.

getSendMessagesAsEmail() - Method in class net.sf.basedb.core.data.UserData

If this flag is set, all messages to this user are sent as an email also, but only if: the server admin has configured an outgoing smtp server and the user has supplied a valid email address.

getSendMessagesAsEmail() - Method in class net.sf.basedb.core.User

If this flag has been set, messges to the user is also sent as an email.

getSeparator() - Method in class net.sf.basedb.clients.web.taglib.path.Path

getSeparator() - Method in class net.sf.basedb.clients.web.taglib.table.CellValue

getSeriesCount() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset

getSeriesKey(int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset

getServer() - Method in class net.sf.basedb.core.data.JobAgentData

Get the server name or ip that this jobagent is running on.

getServer() - Method in class net.sf.basedb.core.data.JobData

The name of the server where the job is executing.

getServer() - Method in class net.sf.basedb.core.Job

Get the name of the server where the job is executing.

getServer() - Method in class net.sf.basedb.core.JobAgent

Get the name or IP-adress of the server were the job agent is running.

getServerAliases(String, Principal[]) - Method in class net.sf.basedb.util.ssl.StaticKeyManager

getServerAndNode() - Method in class net.sf.basedb.core.Job

Utility method for getting both the server and node as a single string (for display purposes).

getServerCertificate() - Method in class net.sf.basedb.core.data.FileServerData

Get the public server certificate indicating that we should trust https connections to the server.

getServerCertificate() - Method in class net.sf.basedb.core.FileServer

Get the public server certificate that indicates that we should only trust the server if it can present a certificate that matches this.

getServerCertificate() - Method in class net.sf.basedb.util.uri.ConnectionParameters

Get the public server certificate that indicates that we should only trust the server if it can present a certificate that matches this.

getServerInfo() - Method in class net.sf.basedb.core.File

getServerName() - Method in class net.sf.basedb.clients.jobagent.Agent

Get the host name of the server where the job agent is running.

getServerName() - Method in class net.sf.basedb.clients.web.taglib.Page

getServerX509Certificate() - Method in class net.sf.basedb.core.FileServer

Get the X.509 certificate for the server.

getServletContext() - Method in class net.sf.basedb.clients.web.extensions.ServletWrapper

getServletName() - Method in class net.sf.basedb.clients.web.extensions.ServletWrapper

getServletPath() - Method in class net.sf.basedb.clients.web.extensions.RequestWrapper

getServlets() - Method in class net.sf.basedb.clients.web.extensions.ServletLoader

Get a list with all loaded servlet definitions.

getServletUrl(String, String) - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Get the base URL for servlets in the extension with the given ID.

getSession() - Method in class net.sf.basedb.core.data.ChangeHistoryData

getSession() - Method in class net.sf.basedb.core.hibernate.SessionWrapper

Deprecated.

getSession() - Method in class net.sf.basedb.core.LogControl

getSession(DbControl) - Method in class net.sf.basedb.core.ChangeHistory

Load the session in which the change was made.

getSession(DbControl) - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo

Load the session in which the change was made.

getSession(DbControl, ChangeHistory, boolean, boolean) - Static method in class net.sf.basedb.clients.web.ChangeHistoryUtil

Get the session in which the changes was made in HTML format.

getSessionControl() - Method in class net.sf.basedb.clients.jobagent.Agent

Get a session control with the configured user logged in.

getSessionControl() - Method in class net.sf.basedb.clients.web.taglib.Page

getSessionControl() - Method in class net.sf.basedb.core.AbstractBatcher

Get the SessionControl object that manages this item.

getSessionControl() - Method in class net.sf.basedb.core.BasicItem

Get the SessionControl object that manages this item.

getSessionControl() - Method in class net.sf.basedb.core.DbControl

Get the SessionControl object that owns this DbControl object.

getSessionControl() - Method in class net.sf.basedb.core.PluginRequest

getSessionControl() - Method in class net.sf.basedb.util.extensions.ClientContext

Get the current session control.

getSessionControl(String, String, String, boolean) - Static method in class net.sf.basedb.core.Application

Get an existing SessionControl object if you know the id.

getSessionControl(PageContext, boolean) - Static method in class net.sf.basedb.clients.web.Base

Get a new or existing SessionControl object given a PageContext.

getSessionControl(ServletRequest, boolean) - Static method in class net.sf.basedb.clients.web.Base

Get a session control for the BASE web client "net.sf.basedb.clients.web".

getSessionControl(ServletRequest, String, boolean) - Static method in class net.sf.basedb.clients.web.Base

Get a new or existing SessionControl object given a ServletRequest instance.

getSessionFactory() - Method in class net.sf.basedb.core.hibernate.SessionWrapper

getSessionFactory() - Static method in class net.sf.basedb.core.HibernateUtil

Get the configured session factory.

getSessionId() - Method in class net.sf.basedb.core.ChangeHistory

Get the ID of the session in which the change was made.

getSessionId() - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo

Get the ID of the session the transaction.

getSessionId() - Method in class net.sf.basedb.core.data.ChangeHistoryData

The ID of the session in which the changes happened.

getSessionId() - Method in class net.sf.basedb.core.log.TransactionDetails

Get the ID of the session or 0 if no user is logged in.

getSessions() - Method in class net.sf.basedb.core.data.ClientData

This is the invers end.

getSessions() - Method in class net.sf.basedb.core.data.UserData

This is the inverse end.

getSessions() - Method in class net.sf.basedb.core.data.UserDeviceData

This is the inverse end but we do not map with inverse="true" cascade="delete" since we want Hibernate to set SessionData.device_id = null instead of deleting sessions.

getSessions() - Method in class net.sf.basedb.core.UserDevice

Get a query for loading login session from this device.

getSessionSetting(String) - Method in class net.sf.basedb.core.SessionControl

Get the value of a session setting with the specified name.

getSet(Map<String, Set<String>>, String) - Method in class net.sf.basedb.clients.web.extensions.JspContext

Get the Set that is stored under the given key.

getSetParameterMethod(Class<?>) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader

Check if the bean class has a setParameter(String, String) method and return it's reference if it has.

getSetter() - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter

getSetterMethod(Class<?>, String) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader

Get the setter method for a given tag name.

getSetterMethodNameFromTag(String) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader

Convert the tag name to a setter method name.

getSetting(String) - Method in class net.sf.basedb.core.ItemContext

Get a value.

getSetting(String) - Method in class net.sf.basedb.core.Presets.Preset

Get the value for the setting with the specified name.

getSetting(String, String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Get a configuration setting for an extension.

getSetting(String, String) - Method in class net.sf.basedb.core.ItemContext

Get a value from the settings or the default value if no current value exists.

getSetting(String, String) - Method in class net.sf.basedb.util.extensions.manager.Settings

Get a configuration setting for an extension.

getSettings() - Method in class net.sf.basedb.core.data.ContextData

Get a map for other settings.

getSettings() - Method in class net.sf.basedb.core.JobAgent

Get a query that returns all plugin-specific settings for this job agent.

getSettings() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager

Get the settings for the extension manager.

getSettings(Job) - Method in class net.sf.basedb.core.JobAgent

Get the settings for the plugin that is used for the specified job.

getSettings(PluginDefinition, boolean) - Method in class net.sf.basedb.core.JobAgent

Get the settings for the specified plugin.

getSettingsForExtension(String) - Method in class net.sf.basedb.util.extensions.manager.Settings

Get a preset containing settings for the given extesion.

getSeverity(ValidationRuleAction) - Method in class net.sf.basedb.util.overview.ValidationOptions

Get the severity level for the specified validator rule.

getShareableItems() - Static method in class net.sf.basedb.core.Metadata

Get a set containing all Shareable item types.

getSharedParent() - Method in class net.sf.basedb.core.ArrayDesignBlock

getSharedParent() - Method in class net.sf.basedb.core.ArrayDesignPlate

getSharedParent() - Method in class net.sf.basedb.core.BioAssay

Get the experiment.

getSharedParent() - Method in class net.sf.basedb.core.BioAssaySet

Get the experiment.

getSharedParent() - Method in class net.sf.basedb.core.BioMaterialEvent

getSharedParent() - Method in class net.sf.basedb.core.BioPlateEventParticipant

getSharedParent() - Method in class net.sf.basedb.core.BioWell

getSharedParent() - Method in class net.sf.basedb.core.ChildItem

Get the shareable parent item of this child item.

getSharedParent() - Method in class net.sf.basedb.core.DataCube

Get the experiment.

getSharedParent() - Method in class net.sf.basedb.core.DataCubeColumn

Get the experiment.

getSharedParent() - Method in class net.sf.basedb.core.DataCubeExtraValue

Get the experiment.

getSharedParent() - Method in class net.sf.basedb.core.DataCubeFilter

Get the experiment.

getSharedParent() - Method in class net.sf.basedb.core.DataCubeLayer

Get the experiment.

getSharedParent() - Method in class net.sf.basedb.core.ExtraValue

Get the experiment.

getSharedParent() - Method in class net.sf.basedb.core.Help

getSharedParent() - Method in class net.sf.basedb.core.JobAgentSettings

getSharedParent() - Method in class net.sf.basedb.core.PlateEvent

getSharedParent() - Method in class net.sf.basedb.core.PlateEventType

getSharedParent() - Method in class net.sf.basedb.core.RootRawBioAssay

Get the experiment.

getSharedParent() - Method in class net.sf.basedb.core.SyncFilter

getSharedParent() - Method in class net.sf.basedb.core.Transformation

Get the experiment.

getSharedParent() - Method in class net.sf.basedb.core.VirtualDb

Get the experiment.

getSharedParent() - Method in class net.sf.basedb.core.Well

getSharedPermissions(ShareableData) - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring

Return 0.

getSharedPermissions(ShareableData) - Method in class net.sf.basedb.core.Job.SignalKeyring

Return 0.

getSharedPermissions(ShareableData) - Method in class net.sf.basedb.core.Keyring

getSharedPermissions(ShareableData) - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring

Return 0.

getSharedPermissions(ShareableData) - Method in class net.sf.basedb.core.SessionControl

Get the shared permissions for a ShareableData object.

getSharedTo(DbControl, SharedItem) - Static method in class net.sf.basedb.util.ShareableUtil

Gets a list with the projects, groups and users(in that order) that an item is shared to.

getShareToEveryOneKey(DbControl, Permission) - Static method in class net.sf.basedb.core.ItemKey

Get a key that can be used to share items to the EVERYONE group with the given permissions.

getSheet() - Method in class net.sf.basedb.util.excel.XlsxTableWriter

Get the current sheet in the workbook.

getSheetAsCsv(int) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil

Convert the given sheet to an CSV InputStream.

getSheetAsCsv(String) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil

Convert the given named sheet to a CSV InputStream.

getSheetNames() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil

Get the names of the sheets in the workbook.

getShort(int) - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult

getShort(int) - Method in class net.sf.basedb.core.DynamicResultIterator.SqlResultImpl

getShort(int) - Method in interface net.sf.basedb.core.query.SqlResult

Get the value of the specified column as a short.

getShortEntityName(String) - Static method in class net.sf.basedb.core.HibernateUtil

Removes the package name part of a class name and any ending 'Data'.

getShortName() - Method in class net.sf.basedb.core.AnnotationTypeCategory

A short name can be used in some places instead of the normal name.

getShortName() - Method in class net.sf.basedb.core.data.AnnotationTypeCategoryData

A short name can be used in some places instead of the normal name.

getShortName() - Method in class net.sf.basedb.plugins.executor.AbstractIOSupport

A default implementation to maintain backwards compatibility.

getShortName() - Method in class net.sf.basedb.plugins.executor.BaseFileExporterSupport

getShortName() - Method in class net.sf.basedb.plugins.executor.BaseFileImporterSupport

getShortName() - Method in class net.sf.basedb.plugins.executor.BfsExporterSupport

getShortName() - Method in class net.sf.basedb.plugins.executor.BfsImporterSupport

getShortName() - Method in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport

getShortName() - Method in interface net.sf.basedb.plugins.executor.IOSupport

Get a short name of the plug-in.

getShortPermissions(Identifiable) - Static method in class net.sf.basedb.clients.web.PermissionUtil

getShow() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

getShow() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn

getShowclazz() - Method in class net.sf.basedb.clients.web.taglib.HideableSection

getShowClazz() - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory.Section

getShowClazz() - Method in interface net.sf.basedb.clients.web.extensions.section.SectionAction

Additional class attribute of the main section tag that is used when the section is visible.

getShowClazz() - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean

getSignal() - Method in exception net.sf.basedb.core.signal.UnsupportedSignalException

Get the signal that is not supported.

getSignal(String) - Static method in class net.sf.basedb.core.signal.Signal

Get the signal with a given ID.

getSignalHandler() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport

getSignalHandler() - Method in interface net.sf.basedb.core.signal.SignalTarget

Get the signal handler that is handling signals on behalf of this object.

getSignalHandler() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

Create a new ThreadSignalHandler that supports the Signal.ABORT signal.

getSignalHandler() - Method in class net.sf.basedb.plugins.Base1PluginExecuter

getSignalHandler() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin

getSignalHandler() - Method in class net.sf.basedb.plugins.BfsExporterPlugin

getSignalHandler() - Method in class net.sf.basedb.plugins.CdfFileReporterImporter

getSignalHandler() - Method in class net.sf.basedb.plugins.CloneReportersPlugin

getSignalHandler() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

getSignalHandler() - Method in class net.sf.basedb.plugins.FormulaFilter

getSignalHandler() - Method in class net.sf.basedb.plugins.GalExporter

getSignalHandler() - Method in class net.sf.basedb.plugins.HelpExporter

getSignalHandler() - Method in class net.sf.basedb.plugins.HelpImporter

getSignalHandler() - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin

getSignalHandler() - Method in class net.sf.basedb.plugins.JepExtraValueCalculator

getSignalHandler() - Method in class net.sf.basedb.plugins.JepIntensityTransformer

getSignalHandler() - Method in class net.sf.basedb.plugins.LowessNormalization

getSignalHandler() - Method in class net.sf.basedb.plugins.MedianRatioNormalization

getSignalHandler() - Method in class net.sf.basedb.plugins.PackedFileExporter

getSignalHandler() - Method in class net.sf.basedb.plugins.PlateMappingExporter

getSignalHandler() - Method in class net.sf.basedb.plugins.PluginConfigurationExporter

getSignalHandler() - Method in class net.sf.basedb.plugins.PluginConfigurationImporter

getSignalHandler() - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker

getSignalHandler(String) - Method in class net.sf.basedb.core.signal.AbstractSignalReceiver

Get the signal handler with a given ID.

getSignalReceiver() - Method in class net.sf.basedb.clients.jobagent.Agent

Get the signal receiver that is processing signal messages on behalf of this job agent.

getSignalReceiver() - Static method in class net.sf.basedb.core.InternalJobQueue

Get the signal receiver used by the internal job queue.

getSignalReceiver(String) - Static method in class net.sf.basedb.core.signal.LocalSignalReceiver

Get a signal receiver with a given ID.

getSignals() - Static method in class net.sf.basedb.core.signal.Signal

Get all registered signals.

getSignals() - Method in exception net.sf.basedb.core.signal.SignalReceivedException

Get the signals that has been received.

getSignalTransporter() - Method in class net.sf.basedb.core.data.JobData

Identifies the signal transporter to use.

getSignalTransporter() - Method in class net.sf.basedb.core.Job

Create and initialise a signal transporter object that can be used to send signal to the plug-in running this job.

getSignalTransporterClass() - Method in class net.sf.basedb.clients.web.util.SimpleSignalProgressReporter

This class does not need any signal transporter.

getSignalTransporterClass() - Method in class net.sf.basedb.core.signal.LocalSignalReceiver

getSignalTransporterClass() - Method in interface net.sf.basedb.core.signal.SignalReceiver

Get the signal transporter class that should be used to send signals to this receiver.

getSignalTransporterClass() - Method in class net.sf.basedb.core.signal.SocketSignalReceiver

getSignalURI() - Method in class net.sf.basedb.core.signal.AbstractSignalTransporter

Get the URI representation of the global signal ID.

getSize() - Method in class net.sf.basedb.core.data.FileData

Get the size in bytes for this FileData object.

getSize() - Method in class net.sf.basedb.core.data.ItemListData

The number of biomaterials in the list.

getSize() - Method in class net.sf.basedb.core.data.PhysicalBioAssayData

The number size of the bioassay.

getSize() - Method in class net.sf.basedb.core.data.ReporterListData

The number of reporter in the list.

getSize() - Method in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo

getSize() - Method in class net.sf.basedb.core.File

Get the (uncompressed) size of this file.

getSize() - Method in class net.sf.basedb.core.ItemList

Get the number of members in this list.

getSize() - Method in class net.sf.basedb.core.PhysicalBioAssay

Get the size of the bioassay.

getSize() - Method in class net.sf.basedb.core.ReporterList

Get the number of reporter in this reporter list.

getSize() - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot

Get the number of annotations.

getSize() - Method in class net.sf.basedb.core.VirtualColumn

Get the maximum size of data in the column if it is a string.

getSize() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo

Get the size of the CSV in bytes.

getSize() - Method in class net.sf.basedb.util.importer.BaseFileWrapper

getSize() - Method in class net.sf.basedb.util.importer.DiskFileWrapper

getSize() - Method in interface net.sf.basedb.util.importer.FileWrapper

Get the size of the file.

getSize() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo

Get the file size.

getSize(String) - Method in class net.sf.basedb.util.bfs.BaseInputStreamLocator

getSize(String) - Method in class net.sf.basedb.util.bfs.DiskInputStreamLocator

getSize(String) - Method in interface net.sf.basedb.util.bfs.InputStreamLocator

Get the size in bytes of the given named resource.

getSizeAtLastSync() - Method in class net.sf.basedb.core.data.ItemListData

The size of the item list after the last sync, -1 if it has never been synced.

getSizeAtLastSync() - Method in class net.sf.basedb.core.ItemList

Get the size of the list at the last sync.

getSkinActions() - Method in class net.sf.basedb.clients.web.taglib.Page

Get all skin extension actions.

getSkinContext() - Method in class net.sf.basedb.clients.web.taglib.Page

Get the JSP context used for invoking skin extensions.

getSkippedLines() - Method in class net.sf.basedb.util.parser.FlatFileParser

Get lines that was skipped during the last call to FlatFileParser.nextData() or FlatFileParser.hasMoreData().

getSlot() - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlot

getSlot() - Method in class net.sf.basedb.util.jobagent.JobInfo

Get the slot the job is using on the job agent.

getSlot(Job) - Method in class net.sf.basedb.clients.jobagent.Agent

Find a free slot for executing a job.

getSlot(Job) - Method in class net.sf.basedb.clients.jobagent.slotmanager.InternalSlotManager

getSlot(Job) - Method in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager

getSlot(Job) - Method in interface net.sf.basedb.clients.jobagent.slotmanager.SlotManager

Get a slot for the specified job.

getSlot(Job.ExecutionTime) - Method in class net.sf.basedb.clients.jobagent.slotmanager.InternalSlotManager

Get a slot for a job with the given estimated execution time.

getSlotManagerClass(String) - Method in class net.sf.basedb.clients.jobagent.Agent

Get the class object for the configured slot manager.

getSnapshot() - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil

Get the snapshot for the last annotation found when calling AnnotationLoaderUtil.findAll(AnnotationSetSnapshot).

getSnapshot(DbControl, int) - Method in class net.sf.basedb.core.snapshot.SnapshotManager

Get the annotation snapshot for the annotation set with the given id.

getSnapshotDate() - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot

Get the date and time this snapshot was created.

getSnapshotManager() - Method in class net.sf.basedb.clients.web.ExperimentExplorer

Get the snapshot manager that is used to load annotation values.

getSnapshotManager() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

Get the current snapshot manager.

getSnapshotManager() - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter

Get the snapshot manager to use with annotation-based fields.

getSnapshotManager() - Method in class net.sf.basedb.util.overview.GenericOverview

Get the current snapshot manager.

getSnapshotManager() - Method in interface net.sf.basedb.util.overview.OverviewContext

Get the snapshot manager that is used to load annotation values.

getSnapshots() - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil

Get all snapshots found by the last AnnotationLoaderUtil.findAll(AnnotationSetSnapshot) call.

getSoftware() - Method in class net.sf.basedb.core.data.DerivedBioAssayData

Get the software used to create this bioassay set.

getSoftware() - Method in class net.sf.basedb.core.data.RawBioAssayData

Get the software used to analyse the scanned image and produce the raw data.

getSoftware() - Method in class net.sf.basedb.core.DerivedBioAssay

Get the Software that was used when creating this bioassay set.

getSoftware() - Method in class net.sf.basedb.core.RawBioAssay

Get the Software used while analysing the scanned images.

getSortable() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn

getSortby() - Method in class net.sf.basedb.clients.web.taglib.table.Table

getSortDirection() - Method in class net.sf.basedb.core.data.ContextData

Get the sort direction, 0 = ascending, 1 = descending

getSortDirection() - Method in class net.sf.basedb.core.ItemContext

If the items are sorted in ascending or descending order.

getSortDirection(String) - Method in class net.sf.basedb.clients.web.taglib.table.Table

Get the sort direction on the given column.

getSortedRawDataTypes(Comparator<RawDataType>) - Static method in class net.sf.basedb.core.RawDataTypes

Get all raw data types sorted according to the given comparator.

getSortOrder() - Method in class net.sf.basedb.core.ItemContext

Get the current sort property as an Order instance.

getSortproperty() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

getSortProperty() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

getSortProperty() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction

Override the default property when this column is used for sorting.

getSortProperty() - Method in class net.sf.basedb.core.data.ContextData

Get property name to sort on.

getSortProperty() - Method in class net.sf.basedb.core.ItemContext

Get the name of the property the current listing is sorted by.

getSource() - Method in class net.sf.basedb.core.Annotation

Get the annotation source.

getSource() - Method in class net.sf.basedb.core.data.AnnotationData

The annotation source. 0 = primary, 1 = inherited, 2 = cloned For primary annotations, only one annotation per annotation type is supported.

getSource() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink

getSource() - Method in class net.sf.basedb.core.data.TransformationData

Get the source bioassayset for the transformation.

getSource() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

Get the source of the annotation.

getSource() - Method in class net.sf.basedb.core.Transformation

Get the source bioassayset used by this transformation.

getSource() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

Get the source bioassay set.

getSource() - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter

Get the source bioassay set.

getSourceBioAssays(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

Gets a list of bioassays that were selected from the current bioassay set, to use for the analysis.

getSourceBioAssaySet(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

Get the bioassay set that is used as the source for the plugin.

getSourceBioAssaySetParameter(String, String) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

Get a plugin parameter that asks for a bioassay set to use as data source for the plugin.

getSourceBioAssaysParameter(String, String) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

Gets a plugin parameter that asks for a subset of bioassays to use as data source for the plugin.

getSourceCoordinate(MappingCoordinate) - Method in class net.sf.basedb.core.PlateMapping

Get the source coordinate for a given destination coordinate.

getSourceCount() - Method in class net.sf.basedb.core.data.PlateMappingData

The required number of source plates.

getSourceCount() - Method in class net.sf.basedb.core.PlateMapping

Get the number of required source plates.

getSourceDerivedBioAssay(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

Get the derived bioassay that is used as the source for the plugin.

getSourceDerivedBioAssayParameter(String, String) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

Get a plugin parameter that asks for a derived bioassay to use as data source for the plugin.

getSourceFileWrapper() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter

Get the source file.

getSourceGeometry() - Method in class net.sf.basedb.core.data.PlateMappingData

The required geometry of source plates in this mapping.

getSourceGeometry() - Method in class net.sf.basedb.core.PlateMapping

Get the PlateGeometry that is required for source plates.

getSourceIndex(Plate) - Method in class net.sf.basedb.core.Plate

If this plate was created by a PlateMapping and the specified plate is a parent, get the index of the parent plate in the list of source plates used by the plate mapping.

getSourceIntensityTransform() - Method in class net.sf.basedb.core.data.FormulaData

A flag indicating what kind of spot source data that the formula can be used with, or null if the formula can be used with any kind of source data. 0 = no transformation; 1 = 2-log; 2 = 10-log

getSourceIntensityTransform() - Method in class net.sf.basedb.core.Formula

Get the intensity transformation that is required on spot data if this formula should generate the correct result.

getSourceItemMustExist() - Method in class net.sf.basedb.core.SyncFilter

If set, a source item that matches the filter must exist, otherwise it must not exist.

getSourceItemTransform() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData

The transform to use for converting filter matches to list members. 0 = none; 1 = parent to child, 2 = child to parent

getSourceItemTransformation() - Method in class net.sf.basedb.core.SyncFilter

Get the transformation to use for converting the items matching this filter to list members.

getSourceItemType() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData

Get the type of items that this filter is applies to.

getSourceItemType() - Method in class net.sf.basedb.core.SyncFilter

Get the source item type that this synchronization filter applies to.

getSourceItemType() - Method in class net.sf.basedb.util.listable.AbstractSourceItemTransformer

getSourceItemType() - Method in class net.sf.basedb.util.listable.PushToParentsTransformer

getSourceItemType() - Method in interface net.sf.basedb.util.listable.SourceItemTransformer

Get the item type of the source items.

getSourceItemType() - Method in class net.sf.basedb.util.listable.SourceItemTransformerChain

Get the source item type of the first step in the chain.

getSourceItemType() - Method in class net.sf.basedb.util.listable.SourceItemTransformerWithCache.TransformerWithCache

getSourceMustExist() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData

If set, the source item must exist, otherwise it must not exist.

getSources() - Method in class net.sf.basedb.core.BioMaterialEvent

Get a query that return all biomaterials used as sources for this event.

getSources() - Method in class net.sf.basedb.core.data.BioMaterialEventData

Get a map containing information about the source biomaterials used in the event.

getSourceType() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

Get the source item type.

getSourceType() - Method in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget

getSpacingX() - Method in class net.sf.basedb.core.ArrayDesignBlock

Get the x spacing between the spots in the slide.

getSpacingX() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData

Get the x spacing.

getSpacingX() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock

getSpacingY() - Method in class net.sf.basedb.core.ArrayDesignBlock

Get the y spacing between the spots in the slide.

getSpacingY() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData

Get the y spacing.

getSpacingY() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock

getSpecification() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn

Get the specification for this column.

getSpotBatcher() - Method in class net.sf.basedb.core.BioAssaySet

Get a batcher used to insert spot data for this bioassayset.

getSpotCount(int) - Method in class net.sf.basedb.core.BioAssaySet

Get the number of spots in a single bioassay.

getSpotData() - Method in class net.sf.basedb.core.BioAssay

Get a query that returns spot data for this bioassay.

getSpotData() - Method in class net.sf.basedb.core.BioAssaySet

Get a query that returns spot data for this bioassayset.

getSpotExtraValueBatcher(Class<I>, ExtraValueType, Job) - Method in class net.sf.basedb.core.BioAssaySet

Get a batcher that is used to insert extra values per spot of the specified type.

getSpotField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.AdvancedFieldConverter

getSpotField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.Base1FieldConverter

Convert a spot field.

getSpotField(String, boolean) - Method in interface net.sf.basedb.util.export.spotdata.ExportableFieldConverter

Create a spot dynamic field for the given name.

getSpotField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.StandardFieldConverter

Find a spot dynamic field.

getSpotFields() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

Get the list of registered spot fields, in the order they were registered.

getSpotFields() - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter

getSpotFields() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter

getSpotFields(BioAssaySet) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin

getSpotFields(BioAssaySet) - Method in class net.sf.basedb.plugins.BfsExporterPlugin

getSpotIntensityParser() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo

Get the spot intensity parser that should be used for parsing spot intensities in this section.

getSpotQuery(boolean) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

Get a configured query for spot data that returns all fields that has been registered with AbstractBioAssaySetExporter.addSpotField(DynamicField).

getSpotQuery(DbControl, int, int, List<TableColumn>) - Method in class net.sf.basedb.clients.web.ExperimentExplorer

Get a query returning spot data for a given reporter and position.

getSpots() - Method in class net.sf.basedb.core.data.RawBioAssayData

The number of data spots in this raw bio assay, that are stored in the database.

getSpots() - Method in class net.sf.basedb.core.RawBioAssay

Utility method that either returns the number of db spots or the number of file spots.

getSpotSectionInfo(int) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo

Get information about a spot section.

getSql() - Method in class net.sf.basedb.core.AnnotationBatcher.InsertBatcher

The SQL statement this batcher is executing.

getSql() - Method in class net.sf.basedb.core.AnnotationBatcher.UpdateBatcher

The SQL statement this batcher is executing.

getSql() - Method in class net.sf.basedb.core.hibernate.ResultSetWork

The sql that is executed by this work.

getSql() - Method in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget

getSqlSymbol() - Method in enum class net.sf.basedb.core.Operator

Get the SQL symbol for this operator.

getSqlType() - Method in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo

getSQLType() - Method in class net.sf.basedb.core.hibernate.TypeWrapper

Get the SQL code for database columns that can store this type.

getSQLType() - Method in enum class net.sf.basedb.core.Type

Get the type of this parameter as specified by the java.sql.Types class.

getSqlTypeCode() - Method in class net.sf.basedb.core.BatchedPropertyInfo

Get the sql type code as defined by Types.

getSqrt() - Method in class net.sf.basedb.core.query.QuadraticMeanExpression

getSshFingerprint() - Method in class net.sf.basedb.core.data.FileServerData

Get the fingerprint of the SSH public key for the server that must be verified when (if) it is accessed via the SSH protocol.

getSshFingerprint() - Method in class net.sf.basedb.core.FileServer

getSshFingerprint() - Method in class net.sf.basedb.util.uri.ConnectionParameters

Get the SSH fingerprint of the server.

getSshPrivateKey() - Method in class net.sf.basedb.core.data.FileServerData

Get the SSH private key that we need to send to the server to make the server accept our connection.

getSshPrivateKey() - Method in class net.sf.basedb.core.FileServer

Get the private key that BASE should use to authenticate with the server when connecting with SSH.

getSshPrivateKey() - Method in class net.sf.basedb.util.uri.ConnectionParameters

Get the private key that should be used to authenticate with the server when connecting using SSH.

getSshPrivateKeyFormat() - Method in class net.sf.basedb.core.data.FileServerData

Get the private key format.

getSshPrivateKeyFormat() - Method in class net.sf.basedb.core.FileServer

Get the format of the SSH private key.

getSshPrivateKeyFormat() - Method in class net.sf.basedb.util.uri.ConnectionParameters

Get the format of the SSH private key (if known).

getSshPrivateKeyPassword() - Method in class net.sf.basedb.core.data.FileServerData

Get the password that is used to unlock the SSH private key.

getSshPrivateKeyPassword() - Method in class net.sf.basedb.core.FileServer

Get the password that is needed to unlock the SSH private key.

getSshPrivateKeyPassword() - Method in class net.sf.basedb.util.uri.ConnectionParameters

Get the password that is needed to unlock the SSH private key.

getSSLContext(byte[], byte[], String) - Static method in class net.sf.basedb.util.ssl.SSLUtil2

Create a SSL context that optionally uses the given trusted server certificate and client certificate.

getSSLSocketFactory() - Static method in class net.sf.basedb.util.ssl.SSLUtil2

Get a SSL Socket Factory object that is used to create SSL sockets.

getSSLSocketFactory(byte[], byte[], String) - Static method in class net.sf.basedb.util.ssl.SSLUtil2

Create a SSL socket factory that optionally uses the given trusted server certificate and client certificate.

getSSLSocketFactory2() - Method in class net.sf.basedb.core.FileServer

Get a socket factory that can be used to create SSL connections to the given server.

getStacktrace() - Method in class net.sf.basedb.util.extensions.logging.LogEntry

Get the stacktrace of the log entry.

getStackTrace() - Method in class net.sf.basedb.core.data.JobData

Get the stack trace in case of an error

getStackTrace() - Method in class net.sf.basedb.core.Job

Get the stack trace in case the job ended with an error

getStartDate() - Method in class net.sf.basedb.core.data.NewsData

Get the first day this news item should be shown.

getStartDate() - Method in class net.sf.basedb.core.News

Get the start date and time for this news item to be published.

getStarted() - Method in class net.sf.basedb.core.data.JobData

Get the date and time the job was started or null if the job hasn't been started.

getStarted() - Method in class net.sf.basedb.core.Job

Get the date and time the job was started.

getStartTime() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults

Get the start time of the scan as a millisecond value.

getStartX() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin

getStartX(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset

getStartXValue(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset

getStartY(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset

getStartYValue(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset

getState() - Method in class net.sf.basedb.core.log.EntityDetails

Get an array with the current state of the entity.

getState() - Method in class net.sf.basedb.core.plugin.NamespaceRequestWrapper

getState() - Method in interface net.sf.basedb.core.plugin.Request

Get state information that was previously saved by Response.setPause(String, String, java.io.Serializable) or Response.setContinue(String, java.io.Serializable).

getState() - Method in class net.sf.basedb.core.PluginRequest.RequestImpl

getState() - Method in class net.sf.basedb.core.PluginResponse

Get the state information that the plug-in wants to save until it is restarted again.

getState() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper

getStatelessSession() - Method in class net.sf.basedb.core.DbControl

Get a stateless Hibernate session using the same database connection as the regular session.

getStaticCache() - Static method in class net.sf.basedb.core.Application

Get the static cache mananger.

getStaticRules() - Static method in class net.sf.basedb.util.overview.OverviewUtil

Get all static (built-in) validation rules grouped by relationship.

getStatistics() - Method in class net.sf.basedb.core.hibernate.SessionWrapper

getStatistics(String) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup

Get the sum of all values added with the ExperimentExplorer.AnnotationGroup.addStatistics(String, float) method with the given key.

getStatistics(DbControl) - Static method in class net.sf.basedb.core.DiskUsage

getStatus() - Method in class net.sf.basedb.clients.jobagent.AgentController

Get status info about running job agent by sending an info request to the agents r emote control service.

getStatus() - Method in class net.sf.basedb.core.data.JobData

Get the status of the job. 1 = waiting, 2 = running, 3 = completed ok, 4 = error

getStatus() - Method in class net.sf.basedb.core.Job

Get the status of the job.

getStatus() - Method in class net.sf.basedb.core.PluginResponse

Get the status of the response.

getStatus() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults.FileResults

A short status message indicating the completed results on this file.

getStatusMessage() - Method in class net.sf.basedb.core.data.JobData

Get a status message.

getStatusMessage() - Method in class net.sf.basedb.core.Job

Get a message about the current status of the job.

getStdev() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin

Get the standard deviation of all values in this bin.

getStickyCol() - Method in class net.sf.basedb.clients.web.taglib.table.Table

getStorageType() - Method in class net.sf.basedb.core.BioPlateType

Get the subtype of storage location where plates of this type are usually stored.

getStorageType() - Method in class net.sf.basedb.core.data.BioPlateTypeData

Get the subtype of storage location where plates of this type are usually stored.

getStream(String) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile

Get an input stream for reading the resource specified by the given path

getString(boolean) - Method in enum class net.sf.basedb.util.formatter.BooleanFormatter.Type

getString(int) - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult

getString(int) - Method in class net.sf.basedb.core.DynamicResultIterator.SqlResultImpl

getString(int) - Method in interface net.sf.basedb.core.query.SqlResult

Get the value of the specified column as a string.

getString(int) - Method in class net.sf.basedb.util.parser.FlatFileParser.Data

Get the value in the specified column.

getString(int) - Method in class net.sf.basedb.util.parser.FlatFileParser.ExcelData

getString(String) - Static method in class net.sf.basedb.core.Config

Get the configuration setting specified by key as a String value.

getString(String) - Static method in class net.sf.basedb.util.Values

Convert a string to a string, and map NULL to the empty string.

getString(String, boolean, String...) - Method in class net.sf.basedb.util.resources.ResourceBundleWrapper

Utility method for returning the value for the key given by key.0 (variant=false) or key.1 (variant=true) depending on the value of the variant parameter.

getString(String, int, String...) - Method in class net.sf.basedb.util.resources.ResourceBundleWrapper

Utility method for returning the value for the key given by: key.index.

getString(String, String) - Static method in class net.sf.basedb.core.Config

Get the configuration setting specified by key as a String value.

getString(String, String) - Static method in class net.sf.basedb.util.Values

Convert a string to a string.

getString(String, String...) - Method in class net.sf.basedb.util.resources.ResourceBundleWrapper

Get a string value from the bundle.

getString(Collection<?>, String, boolean) - Static method in class net.sf.basedb.util.Values

getString(Collection<T>, String, boolean, Formatter<? super T>) - Static method in class net.sf.basedb.util.Values

getString(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.ColumnMapper

getString(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.CompoundMapper

Get a value by invoking each mapper in the order they appear in the list and concatenating the result.

getString(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.ConstantMapper

getString(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.CropStringMapper

Use the parent mapper to get the string value.

getString(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.JepMapper

getString(FlatFileParser.Data) - Method in interface net.sf.basedb.util.parser.Mapper

Get the value for the line of data as a string.

getString(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.NullIfExceptionMapper

getString(HttpResponse, String, String) - Static method in class net.sf.basedb.util.HttpUtil

getStringFormatter(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory

Get a formattater that is encoding strings for HTML output.

getStringFormatter(SessionControl, boolean) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory

Get the logged in user's formatter for strings.

getStringOrNull(String) - Static method in class net.sf.basedb.util.Values

Convert the empty string ("") to null after removing leading and trailing whitespace.

getStringValue() - Method in enum class net.sf.basedb.core.Type

Get the string value representation of this type.

getStringValues() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink

getStyle() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

getStyle() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction

Optional HTML style attribute that is used to style the column through CSS.

getStyle() - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo

Get a style attribute that can used to style the input field.

getStyle() - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

getStyle() - Method in interface net.sf.basedb.clients.web.extensions.menu.MenuItemAction

Extra CSS style attributes that will be added to the style attribute of the menu item div.

getStyle() - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean

getStyle() - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory.Section

getStyle() - Method in interface net.sf.basedb.clients.web.extensions.section.SectionAction

Extra CSS style attributes that will be added to the style attribute of the main section tag.

getStyle() - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean

getStyle() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory

getStyle() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab

getStyle() - Method in interface net.sf.basedb.clients.web.extensions.tabcontrol.TabAction

Extra CSS style attributes that will be added to the style attribute of the main tab tag.

getStyle() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean

getStyle() - Method in interface net.sf.basedb.clients.web.extensions.toolbar.ButtonAction

Extra CSS style attributes that will be added to the style attribute of the main button tag.

getStyle() - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean

getStyle() - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory

getStyle() - Method in class net.sf.basedb.clients.web.taglib.StylableTag

getStyle() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab

getStyle() - Method in class net.sf.basedb.clients.web.taglib.table.Button.ButtonActionWrapper

getStyle() - Method in class net.sf.basedb.clients.web.taglib.table.Cell

getStyle() - Method in class net.sf.basedb.clients.web.taglib.table.CellValue

getStyles() - Method in class net.sf.basedb.clients.web.taglib.Head

getStylesheets() - Method in class net.sf.basedb.clients.web.extensions.AbstractJspFactory

Get a set with all stylesheet references.

getStylesheets() - Method in class net.sf.basedb.clients.web.extensions.JspContext

Get all stylesheets that has been added to this context.

getStylesheets(String) - Method in class net.sf.basedb.clients.web.extensions.JspContext

Get all stylesheets that has been added to this context by the given extension.

getSubCategories() - Method in class net.sf.basedb.core.data.ItemSubtypeData

This is the inverse end.

getSubCategoriesAnnotationType() - Method in class net.sf.basedb.core.AnnotationTypeCategory

Short-cut for calling getItemSubtype().getSubCategoriesAnnotationType().

getSubCategoriesAnnotationType() - Method in class net.sf.basedb.core.data.ItemSubtypeData

Get the annotation type that should be used to divide this subtype into sub-categories when mapped to annotation type categories.

getSubCategoriesAnnotationType() - Method in class net.sf.basedb.core.ItemSubtype

Get the annotation type that should be used to divide this subtype into sub-categories when mapped to annotation type categories.

getSubCategoriesEnumeration() - Method in class net.sf.basedb.core.AnnotationTypeCategory

Short-cut for calling getSubCategoriesAnnotationType().getValues()

getSubCategoriesValueType() - Method in class net.sf.basedb.core.AnnotationTypeCategory

Short-cut for calling getSubCategoriesAnnotationType().getValueType()

getSubcategory() - Method in class net.sf.basedb.clients.web.taglib.SubtypeSelector

getSubCategory() - Method in class net.sf.basedb.clients.web.SubContext

The new sub-category.

getSubCategory() - Method in class net.sf.basedb.core.data.ContextData

Get the annotation type category that is associated with this context.

getSubCategory(DbControl) - Method in class net.sf.basedb.core.ItemContext

Get the sub-category that is related to this context.

getSubCategoryValues() - Method in class net.sf.basedb.core.AnnotationTypeCategory

Get the list of values that are used to match this category.

getSubCategoryValues() - Method in class net.sf.basedb.core.data.AnnotationTypeCategoryData

The values to match for subcategories.

getSubclass() - Method in class net.sf.basedb.clients.web.taglib.StylableTag

getSubclass() - Method in class net.sf.basedb.clients.web.taglib.table.Cell

getSubcontext() - Method in class net.sf.basedb.clients.web.taglib.table.Table

getSubContext() - Method in class net.sf.basedb.clients.web.ExperimentExplorer

Get the subcontext name used for the ItemContext objects related to this explorer.

getSubContext() - Method in class net.sf.basedb.core.ContextKey

getSubContext() - Method in class net.sf.basedb.core.data.ContextData

Get the subcontext this context belongs to.

getSubContext() - Method in class net.sf.basedb.core.data.ContextIndex

Get the subcontext this Context belongs to.

getSubContext() - Method in class net.sf.basedb.core.data.JobData

The name of the subcontext that was active whjen configuring this job.

getSubContext() - Method in class net.sf.basedb.core.ItemContext

Get the sub-context name of this context.

getSubContext() - Method in class net.sf.basedb.core.plugin.GuiContext

getSubdirectories() - Method in class net.sf.basedb.core.data.DirectoryData

This is the inverse end.

getSubDirectories() - Method in class net.sf.basedb.core.Directory

Get a query that return subdirectories of this directory.

getSubid() - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu

getSubmenuId() - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

getSubmenuId() - Method in interface net.sf.basedb.clients.web.extensions.menu.MenuItemAction

The ID of a new submenu.

getSubmenuId() - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean

getSubtitle() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

getSubtitle() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction

An optional subtitle.

getSubtitle() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

getSubtypableItems() - Static method in class net.sf.basedb.core.Metadata

Get a set containing all Subtypable item types.

getSubtype() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

Get the target subtype from the expression.

getSubtype() - Method in class net.sf.basedb.util.bfs.MetadataModel

Get the BFS subtype.

getSubtype() - Method in class net.sf.basedb.util.bfs.MetadataWriter

Get the BFS subtype.

getSubtypeName() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

Get the name of the targeted subtype.

getSubtypes() - Method in class net.sf.basedb.clients.web.taglib.SubtypeSelector

getSubtypesQuery(Item) - Static method in class net.sf.basedb.clients.web.Base

Get a query that returns all subtypes for the given main item type.

getSuccessMessage() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport

getSuccessMessage() - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin

Called if the export was successful to let the subclass generate a simple message that is sent back to the core and user interface.

getSuccessMessage() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin

getSuccessMessage() - Method in class net.sf.basedb.plugins.BfsExporterPlugin

getSuccessMessage() - Method in class net.sf.basedb.plugins.GalExporter

getSuccessMessage() - Method in class net.sf.basedb.plugins.HelpExporter

getSuccessMessage() - Method in class net.sf.basedb.plugins.HelpImporter

getSuccessMessage() - Method in class net.sf.basedb.plugins.PackedFileExporter

getSuccessMessage() - Method in class net.sf.basedb.plugins.PlateMappingExporter

getSuccessMessage() - Method in class net.sf.basedb.plugins.PluginConfigurationExporter

getSuccessMessage(int) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

Called if the parsing was successful to let the subclass generate a simple message that is sent back to the core and user interface.

getSuccessMessage(int) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter

getSuccessMessage(int) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

getSuccessMessage(int) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

getSuccessMessage(int) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter

getSuccessMessage(int) - Method in class net.sf.basedb.plugins.PlateFlatFileImporter

Return x plates inserted.

getSuccessMessage(int) - Method in class net.sf.basedb.plugins.PlateMappingImporter

Return Platemapping 'name' created..

getSuccessMessage(int) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter

getSuccessMessage(int) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter

Return x spots inserted.

getSuccessMessage(int) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter

Return x new reporters; y updated reporters; z reporters added to list.

getSuccessMessage(int) - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

Return x features inserted; y blocks inserted.

getSuffix() - Method in class net.sf.basedb.clients.web.taglib.table.CellValue

getSuffix() - Static method in class net.sf.basedb.core.Version

Get the version suffix string (eg "-dev" for development versions)

getSuffix() - Method in class net.sf.basedb.util.bfs.SequenceFilenameGenerator

Get the suffix that is used for file name generation.

getSuggestedJobName() - Method in class net.sf.basedb.core.PluginResponse

Get the job name that was suggested by the job.

getSum() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin

Get the sum of all values in this bin.

getSum(int) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup

Get the sum of intensities for the specified channel.

getSummary() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults

Get a summary of the scan results as a textual description.

getSummary(Group) - Method in class net.sf.basedb.core.DiskUsageStatistics

Get a summary of the disk usage for the specified group.

getSummary(User) - Method in class net.sf.basedb.core.DiskUsageStatistics

Get a summary of the disk usage for the specified user.

getSummaryOfUserAgent(String) - Static method in class net.sf.basedb.util.HttpUtil

Get a summary of the user agent: Browser with major version Operating system with version Typy of device (eg. desktop, phone, etc.)

getSupportedSignals() - Method in class net.sf.basedb.core.Job.JobSignalTransporter

getSupportedSignals() - Method in class net.sf.basedb.core.signal.AbstractSignalHandler

getSupportedSignals() - Method in class net.sf.basedb.core.signal.AbstractSignalTransporter

getSupportedSignals() - Method in class net.sf.basedb.core.signal.DelegatingSignalHandler

getSupportedSignals() - Method in interface net.sf.basedb.core.signal.SignalHandler

Get all signals that are supported by this handler.

getSupportedSignals() - Method in interface net.sf.basedb.core.signal.SignalTransporter

Get a collection containing the signals supported, by the signal handler.

getSupportedSourceItems(SyncFilter.SourceItemTransform) - Method in class net.sf.basedb.util.listable.AbstractSourceItemTransformerFactory

getSupportedSourceItems(SyncFilter.SourceItemTransform) - Method in interface net.sf.basedb.util.listable.SourceItemTransformerFactory

Get the supported source item types when transforming in the specified direction.

getSupportedSourceItems(SyncFilter.SourceItemTransform) - Method in class net.sf.basedb.util.listable.SourceItemTransformerWithCache

getSupportsConfigurations() - Method in class net.sf.basedb.core.data.PluginDefinitionData

If the plugin supports configurations or not.

getSupportsDeviceVerification() - Method in class net.sf.basedb.core.Client

This flag indicates if the registered client application supports device verification or not.

getSupportsDeviceVerification() - Method in class net.sf.basedb.core.data.ClientData

A flag indicating if this client application supports device verification.

getSymbol() - Method in class net.sf.basedb.core.data.ReporterData

Get the gene symbol of the reporter.

getSymbol() - Method in class net.sf.basedb.core.data.UnitSymbolData

The symbol, which must be unique for a given quantity.

getSymbol() - Method in enum class net.sf.basedb.core.Operator

Get the symbol for this operator, useful for display in client applications.

getSymbols() - Method in class net.sf.basedb.core.data.QuantityData

This is the inverse end.

getSymbols() - Method in class net.sf.basedb.core.data.UnitData

This is the inverse end.

getSymbols() - Method in class net.sf.basedb.core.Unit

Get all symbols that are registered for this unit.

getSyncDate() - Method in class net.sf.basedb.core.data.ItemListData

Get the date and time the list members was last synchronized by the filter context.

getSyncDate() - Method in class net.sf.basedb.core.ItemList

Get the last sync date+time.

getSyncFilters() - Method in class net.sf.basedb.core.data.ItemListData

This is the inverse end.

getSyncFilters() - Method in class net.sf.basedb.core.ItemList

Get a query returning all synchronization filters for this list

getSynchronizedQuerySpaces() - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

getSyncProperties(ItemListSyncFilterData) - Static method in class net.sf.basedb.core.SyncFilter

Get a string representing the current syncfilter properties that may affect the end result even if the query return the same items.

getSystemId() - Method in class net.sf.basedb.core.BioPlateEventType

getSystemId() - Method in class net.sf.basedb.core.data.BioPlateEventTypeData

getSystemId() - Method in class net.sf.basedb.core.data.DirectoryData

getSystemId() - Method in class net.sf.basedb.core.data.GroupData

getSystemId() - Method in class net.sf.basedb.core.data.ItemSubtypeData

Override the property definition since we may have to update the system id during installation.

getSystemId() - Method in class net.sf.basedb.core.data.QuantityData

getSystemId() - Method in class net.sf.basedb.core.data.QuotaData

getSystemId() - Method in class net.sf.basedb.core.data.QuotaTypeData

getSystemId() - Method in class net.sf.basedb.core.data.RoleData

getSystemId() - Method in interface net.sf.basedb.core.data.SystemData

Get the system id for the item.

getSystemId() - Method in class net.sf.basedb.core.data.UserData

getSystemId() - Method in class net.sf.basedb.core.Directory

getSystemId() - Method in class net.sf.basedb.core.Group

getSystemId() - Method in class net.sf.basedb.core.ItemSubtype

getSystemId() - Method in class net.sf.basedb.core.Quantity

getSystemId() - Method in class net.sf.basedb.core.Quota

getSystemId() - Method in class net.sf.basedb.core.QuotaType

getSystemId() - Method in class net.sf.basedb.core.Role

getSystemId() - Method in interface net.sf.basedb.core.SystemItem

Get the system id for the item.

getSystemId() - Method in class net.sf.basedb.core.User

getTabcontrol() - Method in class net.sf.basedb.clients.web.taglib.Help

getTabindex() - Method in class net.sf.basedb.clients.web.taglib.Button

getTabindex() - Method in class net.sf.basedb.clients.web.taglib.Help

getTabindex() - Method in class net.sf.basedb.clients.web.taglib.Icon

getTabindex() - Method in class net.sf.basedb.clients.web.taglib.Input

getTabindex() - Method in class net.sf.basedb.clients.web.taglib.Select

getTabindex() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab

getTabindex() - Method in class net.sf.basedb.clients.web.taglib.table.Button

getTabindex() - Method in class net.sf.basedb.clients.web.taglib.Zoom

getTabIndex() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory

getTabIndex() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab

getTabIndex() - Method in interface net.sf.basedb.clients.web.extensions.tabcontrol.TabAction

Get the tab index used to control focus order when tabbing.

getTabIndex() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean

getTabIndex() - Method in interface net.sf.basedb.clients.web.extensions.toolbar.ButtonAction

Get the tab index used to control focus order when tabbing.

getTabIndex() - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean

getTabIndex() - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory

getTabIndex() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab

getTabIndex() - Method in class net.sf.basedb.clients.web.taglib.table.Button.ButtonActionWrapper

getTable() - Method in class net.sf.basedb.clients.web.taglib.SubtypeSelector

getTable() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnHeaders

getTable() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnSubtitles

getTable() - Method in class net.sf.basedb.clients.web.taglib.table.Data

getTable() - Method in class net.sf.basedb.clients.web.taglib.table.Headers

getTable() - Method in class net.sf.basedb.clients.web.taglib.table.PropertyFilter

getTable() - Method in class net.sf.basedb.clients.web.taglib.table.Row

getTable() - Method in class net.sf.basedb.clients.web.taglib.table.Rows

getTable() - Method in class net.sf.basedb.core.dbengine.TableInfo

Get the table this information is representing.

getTableInfo(Session, String) - Static method in class net.sf.basedb.core.Update

getTableName() - Method in class net.sf.basedb.core.RawDataType

Get the name of the database table that is used to store the extra properties of this raw data type.

getTableName() - Method in class net.sf.basedb.core.RealTable

Get the unquoted table name of this table in the database.

getTableName() - Method in enum class net.sf.basedb.core.Type

Get the name of the database table, parameter and annotation values of this value type are stored in.

getTableName(VirtualDb) - Method in enum class net.sf.basedb.core.VirtualTable

Get the real table name of this table in the database.

getTag() - Method in class net.sf.basedb.core.data.ExtractData

The tag used for tagging the extract so that it can be tracked on physical bioassays.

getTag() - Method in class net.sf.basedb.core.Extract

Get the tag that has been applied to this extract in order to be able to distinguish it from other extracts on a physical bioassay.

getTargetIds() - Method in class net.sf.basedb.util.listable.TransformCache.CacheEntry

getTargetItem() - Method in class net.sf.basedb.util.listable.AbstractSourceItemTransformerFactory

getTargetItem() - Method in interface net.sf.basedb.util.listable.SourceItemTransformerFactory

Get the target item type of this transformer factory.

getTargetItem() - Method in class net.sf.basedb.util.listable.SourceItemTransformerWithCache

getTargetItemType() - Method in class net.sf.basedb.util.listable.AbstractSourceItemTransformer

getTargetItemType() - Method in class net.sf.basedb.util.listable.PushToParentsTransformer

getTargetItemType() - Method in interface net.sf.basedb.util.listable.SourceItemTransformer

Get the item type of the target items.

getTargetItemType() - Method in class net.sf.basedb.util.listable.SourceItemTransformerChain

Get the target item type of the last step in the chain.

getTargetItemType() - Method in class net.sf.basedb.util.listable.SourceItemTransformerWithCache.TransformerWithCache

getTargetType() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

Get the target ITEMTYPE from the expression.

getTargetType() - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics

Get the item type of the target item for the link.

getTargetTypes() - Method in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget

getTenantIdentifier() - Method in class net.sf.basedb.core.hibernate.SessionWrapper

getTenantIdentifier() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

GetterSetter(PropertyAccessStrategy, Class<?>, String) - Constructor for class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter

Create a new getter or setter.

getTextarea() - Method in class net.sf.basedb.clients.web.taglib.Zoom

getTextValues() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink

getThetaJoin(Query, DbControl) - Method in class net.sf.basedb.core.DynamicJoin

getThetaJoin(Query, DbControl) - Method in class net.sf.basedb.core.ExtraValueJoin

getThetaJoin(Query, DbControl) - Method in class net.sf.basedb.core.query.AnnotationJoin

getThetaJoin(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlInnerJoin

getThetaJoin(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlLeftJoin

getThetaJoin(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlRightJoin

getThetaJoin(Query, DbControl) - Method in interface net.sf.basedb.core.query.Join

getThetaJoin(Query, DbControl) - Method in class net.sf.basedb.core.RealJoin

getThetaJoin(Query, DbControl) - Method in class net.sf.basedb.core.ReporterListJoin

getThetaJoinCondition(Query, DbControl) - Method in class net.sf.basedb.core.DynamicJoin

getThetaJoinCondition(Query, DbControl) - Method in class net.sf.basedb.core.ExtraValueJoin

getThetaJoinCondition(Query, DbControl) - Method in class net.sf.basedb.core.query.AnnotationJoin

getThetaJoinCondition(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlInnerJoin

getThetaJoinCondition(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlLeftJoin

getThetaJoinCondition(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlRightJoin

getThetaJoinCondition(Query, DbControl) - Method in interface net.sf.basedb.core.query.Join

getThetaJoinCondition(Query, DbControl) - Method in class net.sf.basedb.core.RealJoin

getThetaJoinCondition(Query, DbControl) - Method in class net.sf.basedb.core.ReporterListJoin

getThisAnnotation(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

Get the annotation this is a snapshot of.

getThisAnnotationId() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

Get the id of the annotation this is a snapshot of.

getThisAnnotationSet(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

Get the annotation set this annotation belongs to.

getThisAnnotationSetId() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

Get the id of the annotation set this is a snapshot of.

getThisItem(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

Get the item that this annotation belongs to.

getThisItemId() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

Get the id of the item this annotation belongs to.

getThisItemType() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

Get the item type of the item this annotation belongs to.

getThisLastUpdate() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

Get the date+time this annotation was last updated.

getThisUnit(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

Get the unit the annotatation values should use for display.

getThisUnitId() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

Get the id of the unit that the annotation values should use when displayed.

getThisValues() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

Get the annotation values for this annotation.

getThousandsSeparator(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterSettings

Get the separator character to use as a "thousands" separator in large numbers.

getThreadPriority(Job.ExecutionTime) - Method in class net.sf.basedb.clients.jobagent.Agent

Get the thread priority to use for the specified execution time slot.

getTime() - Method in class net.sf.basedb.core.ChangeHistory

Get the date and time the change was made.

getTime() - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo

Get the date and time of the transaction.

getTime() - Method in class net.sf.basedb.core.data.ChangeHistoryData

Get the time of the change.

getTime() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults.FileResults

Get the time of the results as a millisecond value.

getTime(int) - Method in class net.sf.basedb.util.timer.PerformanceTimer

Get the current time of a timer.

getTimeout() - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

getTimeout() - Method in class net.sf.basedb.util.listable.TransformCache.CacheEntry

getTimerTask(TimerTask, boolean) - Method in class net.sf.basedb.util.timer.Scheduler

getTimeSent() - Method in class net.sf.basedb.core.data.MessageData

Get the date and time this message was sent.

getTimeSent() - Method in class net.sf.basedb.core.Message

Get the date and time the message was sent.

getTimestamp() - Method in class net.sf.basedb.util.extensions.logging.LogEntry

The timestamp of the log entry.

getTimestampFormat() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil

Get the date formatter that is used for formatting cells with timestamp-like values.

getTimestampFormatter(String) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

getTimestampMapper(String) - Method in class net.sf.basedb.util.parser.FlatFileParser

Get a mapper using the default timestamp format.

getTimestampValues() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink

getTimstampFormat() - Method in class net.sf.basedb.util.excel.AutoFormatter

getTitle() - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup

Get the title of this annotation group.

getTitle() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

getTitle() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction

The column title.

getTitle() - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

getTitle() - Method in interface net.sf.basedb.clients.web.extensions.menu.MenuItemAction

Get the title of the menu.

getTitle() - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean

getTitle() - Method in interface net.sf.basedb.clients.web.extensions.plot.OverviewPlotAction

The title of the overview plots.

getTitle() - Method in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean

getTitle() - Method in interface net.sf.basedb.clients.web.extensions.plot.PlotGenerator

Get the title of the generated image.

getTitle() - Method in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean

getTitle() - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory.Section

getTitle() - Method in interface net.sf.basedb.clients.web.extensions.section.SectionAction

Get the title of the section.

getTitle() - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean

getTitle() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory

getTitle() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab

getTitle() - Method in interface net.sf.basedb.clients.web.extensions.tabcontrol.TabAction

Get the title of the tab.

getTitle() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean

getTitle() - Method in interface net.sf.basedb.clients.web.extensions.toolbar.ButtonAction

Get the title of the button.

getTitle() - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean

getTitle() - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory

getTitle() - Method in class net.sf.basedb.clients.web.taglib.Button

getTitle() - Method in class net.sf.basedb.clients.web.taglib.HideableSection

getTitle() - Method in class net.sf.basedb.clients.web.taglib.Input

getTitle() - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem

getTitle() - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu

getTitle() - Method in class net.sf.basedb.clients.web.taglib.Page

getTitle() - Method in class net.sf.basedb.clients.web.taglib.path.PathElement

getTitle() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab

getTitle() - Method in class net.sf.basedb.clients.web.taglib.table.Button.ButtonActionWrapper

getTitle() - Method in class net.sf.basedb.clients.web.taglib.table.Button

getTitle() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

getTitle() - Method in class net.sf.basedb.clients.web.taglib.table.Label

getTitle() - Method in class net.sf.basedb.clients.web.taglib.table.Table

getTitle() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn

getTitle() - Method in class net.sf.basedb.clients.web.taglib.Zoom

getTitle() - Method in exception net.sf.basedb.clients.web.WebException

Get the title of the error message.

getTitle() - Static method in class net.sf.basedb.core.Application

Get the "display title" of this server.

getTitle() - Method in class net.sf.basedb.core.data.ExperimentData

Get the title for this experiment.

getTitle() - Method in class net.sf.basedb.core.data.ReporterClonePropertyData

Get the title of the property.

getTitle() - Method in class net.sf.basedb.core.Experiment

Get the title for the publication for this experiment.

getTitle() - Method in class net.sf.basedb.core.ExtendedProperty

Get the title of the extended property.

getTitle() - Method in class net.sf.basedb.core.IntensityFormula

Get the title of the intensity formula.

getTitle() - Method in class net.sf.basedb.core.RequestInformation

Get the title of the request.

getTitle() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField

getTitle() - Method in class net.sf.basedb.plugins.batchimport.AnnotationIdMethod

getTitle() - Method in class net.sf.basedb.plugins.batchimport.FallbackIdMethod

getTitle() - Method in class net.sf.basedb.plugins.batchimport.FileImporter.PathIdMethod

getTitle() - Method in interface net.sf.basedb.plugins.batchimport.IdMethod

The display title of the method.

getTitle() - Method in class net.sf.basedb.plugins.batchimport.InternalIdMethod

getTitle() - Method in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod

getTitle() - Method in class net.sf.basedb.plugins.batchimport.PropertyIdMethod

getTitle() - Method in class net.sf.basedb.util.export.spotdata.AnnotationAssayField

Returns the name of the configured annotation type, or the empty string if not configured.

getTitle() - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField

getTitle() - Method in interface net.sf.basedb.util.export.spotdata.ExportableField

Get the column header.

getTitle() - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField

getTitle() - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField

getTitle() - Method in interface net.sf.basedb.util.overview.extensions.ValidationRuleAction

Get the title of this validator rule.

getTitle() - Method in class net.sf.basedb.util.overview.Node

Get the display title of this node.

getTitle() - Method in class net.sf.basedb.util.overview.Validator

Get the title of this validator.

getTo() - Method in class net.sf.basedb.core.AnyToAny

Get the item this link is linking to.

getTo() - Method in class net.sf.basedb.core.data.MessageData

The user this message is to.

getTo() - Method in class net.sf.basedb.core.Message

Get the User this message was sent to.

getTo(S) - Method in class net.sf.basedb.core.AnyToAny.FastLinkLoader

Get the target item that is linked from the source item by the named link.

getToId() - Method in class net.sf.basedb.core.AnyToAny

Get the ID of the item this link is linking to.

getToId() - Method in class net.sf.basedb.core.data.AnyToAnyData

The ID of the item we are linking to.

getToken() - Method in class net.sf.basedb.core.data.UserDeviceData

Get the device token.

getToolParameters(List<String>) - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator

getToolParameters(List<String>) - Method in class net.sf.basedb.plugins.ManualTransformCreator

getTooltip() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

getTooltip() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction

An optional tooltip that is displayed when the mouse is over the column header.

getTooltip() - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo

Get a tooltip text that is displayed when the user holds the mouse over the input field.

getTooltip() - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

getTooltip() - Method in interface net.sf.basedb.clients.web.extensions.menu.MenuItemAction

A tooltip that is shown as a yellow popup when the user points the mouse at the menu item.

getTooltip() - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean

getTooltip() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory

getTooltip() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab

getTooltip() - Method in interface net.sf.basedb.clients.web.extensions.tabcontrol.TabAction

A tooltip that is shown as a yellow popup when the user points the mouse at the tab.

getTooltip() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean

getTooltip() - Method in interface net.sf.basedb.clients.web.extensions.toolbar.ButtonAction

A tooltip that is shown as a yellow popup when the user points the mouse at the button.

getTooltip() - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean

getTooltip() - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory

getTooltip() - Method in class net.sf.basedb.clients.web.taglib.Button

getTooltip() - Method in class net.sf.basedb.clients.web.taglib.Help

getTooltip() - Method in class net.sf.basedb.clients.web.taglib.Icon

getTooltip() - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem

getTooltip() - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu

getTooltip() - Method in class net.sf.basedb.clients.web.taglib.path.PathElement

getTooltip() - Method in class net.sf.basedb.clients.web.taglib.PropertyValue

getTooltip() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab

getTooltip() - Method in class net.sf.basedb.clients.web.taglib.table.Button.ButtonActionWrapper

getTooltip() - Method in class net.sf.basedb.clients.web.taglib.table.Button

getTooltip() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

getTooltip() - Method in class net.sf.basedb.clients.web.taglib.table.Label

getTooltip() - Method in class net.sf.basedb.clients.web.taglib.Zoom

getTotal() - Method in class net.sf.basedb.core.DiskUsageStatistics.Summary

Get the total disk usage in bytes

getTotal() - Method in class net.sf.basedb.core.SimpleAbsoluteProgressReporter

Get the end point of the task.

getTotal(Location) - Method in class net.sf.basedb.core.DiskUsageStatistics.Summary

Get the total disk usage of the specified location in bytes.

getTotal(QuotaType) - Method in class net.sf.basedb.core.DiskUsageStatistics.Summary

Get the total disk usage for the specified quota type in bytes.

getTotal(QuotaType, Location) - Method in class net.sf.basedb.core.DiskUsageStatistics.Summary

Get the total disk usage of the specified location and quota type in bytes.

getTotalBytes() - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress

Get the total number of bytes expected to upload.

getTotalCount() - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator

getTotalCount() - Method in class net.sf.basedb.core.AbstractResultList

getTotalCount() - Method in class net.sf.basedb.core.DataResultIterator

From the QueryResult interface ---------------------------------

getTotalCount() - Method in class net.sf.basedb.core.DynamicResultIterator

From the QueryResult interface ---------------------------------

getTotalCount() - Method in class net.sf.basedb.core.ItemResultIterator

From the QueryResult interface ---------------------------------

getTotalCount() - Method in interface net.sf.basedb.core.query.QueryResult

Get the total number of items returned by the query, ignoring any limits set by Query.setFirstResult(int) and Query.setMaxResults(int).

getTotalCount() - Method in class net.sf.basedb.core.ReporterScoreResultIterator

From the QueryResult interface ---------------------------------

getTotalCount() - Method in class net.sf.basedb.core.UnmodifiableResultList

getTotalFileSize() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

Get the total file size of all files that are going to be imported.

getTotalFileSize() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter

getTotalInsertCount() - Method in class net.sf.basedb.core.BasicBatcher

Gets the total number of inserts done by the batcher

getTotalInsertCount() - Method in class net.sf.basedb.core.MappingBatcher

Get the total number of mappings to raw data create by this mapper.

getTotalMemory() - Method in class net.sf.basedb.core.JobAgent

Get the total memory in bytes of the server where the job agent is running.

getTotalMemory() - Method in class net.sf.basedb.util.jobagent.JobAgentInfo

Get the total memory on the job agent's server in bytes.

getTotalrows() - Method in class net.sf.basedb.clients.web.taglib.table.Navigator

getTotalSummary() - Method in class net.sf.basedb.core.DiskUsageStatistics

Get a summary of the total disk usage.

getTotalWells() - Method in class net.sf.basedb.core.BioPlate

Get the total number of wells on this plate.

getToType() - Method in class net.sf.basedb.core.AnyToAny.FastLinkLoader

The target item type.

getToType() - Method in class net.sf.basedb.core.AnyToAny

Get the type of the item this link is linking to.

getToType() - Method in class net.sf.basedb.core.data.AnyToAnyData

The type code of the item we are linking to.

getTransaction() - Method in class net.sf.basedb.core.hibernate.SessionWrapper

getTransaction() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

getTransactionDetails() - Method in class net.sf.basedb.core.LogControl

Get information about the current transaction.

getTransactionId() - Method in class net.sf.basedb.core.ChangeHistory

Get the ID of the transaction that initiated the change.

getTransactionId() - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo

Get the ID of the transaction.

getTransactionInfo(DbControl, int) - Static method in class net.sf.basedb.core.ChangeHistory

Load information about a single transaction.

getTransferredBytes() - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress

Get the number of bytes that have been uploaded so far.

getTransformation() - Method in class net.sf.basedb.core.BioAssaySet

Get the transformation that created this bioassayset.

getTransformation() - Method in class net.sf.basedb.core.data.BioAssaySetData

Get the transformation that created this bioassayset.

getTransformation() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter

Get the destination transformation.

getTransformation() - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter

Get the destination transformation.

getTransformationName(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

Generate a name for the transformation based on the plugin and it's configuration.

getTransformationNameParameter(String, String, String) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

Create a plugin parameter that asks for the name of the transformation.

getTransformations() - Method in class net.sf.basedb.core.BioAssaySet

Get a query that return all transformations using this bioassayset as a source.

getTransformations() - Method in class net.sf.basedb.core.data.BioAssaySetData

This is the inverse end.

getTransformations() - Method in class net.sf.basedb.core.data.ExperimentData

This is the inverse end.

getTransformations() - Method in class net.sf.basedb.core.data.JobData

This is the inverse end.

getTransformations() - Method in class net.sf.basedb.core.data.RawBioAssayData

This is the inverse end.

getTransformations() - Method in class net.sf.basedb.core.Experiment

Get a query that return all transformations including root transformations in this experiment.

getTransformer() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn

Get the transformer implementation that is used to turn source item into target items.

getTransformerFactory(Item) - Static method in class net.sf.basedb.util.listable.ListableUtil

Create a source item transformer factory that can transform items to the given target item type.

getTransformerFactory(Item, boolean) - Static method in class net.sf.basedb.util.listable.ListableUtil

Create a source item transformer factory that can transform items to the given target item type.

getTray() - Method in class net.sf.basedb.core.BioPlate

Get the tray within the "storage location" for this bioplate.

getTray() - Method in class net.sf.basedb.core.data.BioPlateData

Get the tray in the storage location were the bioplate is stored.

getType() - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext

Get the context type that the file is being displayed in.

getType() - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

getType() - Method in interface net.sf.basedb.clients.web.extensions.menu.MenuItemAction

The type of menu item.

getType() - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean

getType() - Method in class net.sf.basedb.clients.web.taglib.Input

getType() - Method in class net.sf.basedb.clients.web.taglib.menu.Menu

getType() - Method in class net.sf.basedb.core.Annotation

getType() - Method in class net.sf.basedb.core.AnnotationSet

getType() - Method in class net.sf.basedb.core.AnnotationType

getType() - Method in class net.sf.basedb.core.AnnotationTypeCategory

getType() - Method in class net.sf.basedb.core.AnyToAny

getType() - Method in class net.sf.basedb.core.ArrayBatch

getType() - Method in class net.sf.basedb.core.ArrayDesign

getType() - Method in class net.sf.basedb.core.ArrayDesignBlock

getType() - Method in class net.sf.basedb.core.ArrayDesignPlate

getType() - Method in class net.sf.basedb.core.ArraySlide

getType() - Method in class net.sf.basedb.core.BasicBatcher

Get the type of item supported by the batcher.

getType() - Method in class net.sf.basedb.core.BioAssay

getType() - Method in class net.sf.basedb.core.BioAssaySet

getType() - Method in class net.sf.basedb.core.BioMaterialEvent

getType() - Method in class net.sf.basedb.core.BioPlate

getType() - Method in class net.sf.basedb.core.BioPlateEvent

getType() - Method in class net.sf.basedb.core.BioPlateEventParticipant

getType() - Method in class net.sf.basedb.core.BioPlateEventType

getType() - Method in class net.sf.basedb.core.BioPlateType

getType() - Method in class net.sf.basedb.core.BioSource

getType() - Method in class net.sf.basedb.core.BioWell

getType() - Method in class net.sf.basedb.core.ChangeHistory

getType() - Method in class net.sf.basedb.core.Client

getType() - Method in class net.sf.basedb.core.ClientDefaultSetting

getType() - Method in class net.sf.basedb.core.data.FormulaData

The type of formula: 1 = intensity expression; raw data type required, 1 formula for each channel 2 = intensity transformation; raw data type or channels required, 1 formula for each channel 3 = column expression; raw data type or channels required, 1 formula only 4 = column restriction; raw data type or channels required, 1 formula only

getType() - Method in class net.sf.basedb.core.data.JobData

The type of job: 1 = run plugin, 2 = other

getType() - Method in class net.sf.basedb.core.DataCube

getType() - Method in class net.sf.basedb.core.DataCubeColumn

getType() - Method in class net.sf.basedb.core.DataCubeExtraValue

getType() - Method in class net.sf.basedb.core.DataCubeFilter

getType() - Method in class net.sf.basedb.core.DataCubeLayer

getType() - Method in class net.sf.basedb.core.DataFileType

getType() - Method in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo

getType() - Method in class net.sf.basedb.core.DerivedBioAssay

getType() - Method in class net.sf.basedb.core.Directory

getType() - Method in class net.sf.basedb.core.DiskUsage

getType() - Method in class net.sf.basedb.core.Experiment

getType() - Method in class net.sf.basedb.core.ExtendedProperty

Get the type of the extended property.

getType() - Method in class net.sf.basedb.core.Extract

getType() - Method in class net.sf.basedb.core.ExtraValue

getType() - Method in class net.sf.basedb.core.ExtraValueType

getType() - Method in class net.sf.basedb.core.FeatureBatcher

getType() - Method in class net.sf.basedb.core.File

getType() - Method in class net.sf.basedb.core.FileServer

getType() - Method in class net.sf.basedb.core.FileSet

getType() - Method in class net.sf.basedb.core.FileSetMember

getType() - Method in class net.sf.basedb.core.Formula

getType() - Method in class net.sf.basedb.core.GlobalDefaultSetting

getType() - Method in class net.sf.basedb.core.Group

getType() - Method in class net.sf.basedb.core.Hardware

getType() - Method in class net.sf.basedb.core.Help

getType() - Method in interface net.sf.basedb.core.Identifiable

Get the type of item represented by the object.

getType() - Method in class net.sf.basedb.core.ItemKey

getType() - Method in class net.sf.basedb.core.ItemList

getType() - Method in class net.sf.basedb.core.ItemProxy

getType() - Method in class net.sf.basedb.core.ItemSubtype

getType() - Method in class net.sf.basedb.core.ItemSubtypeFileType

getType() - Method in class net.sf.basedb.core.Job

getType() - Method in class net.sf.basedb.core.JobAgent

getType() - Method in class net.sf.basedb.core.JobAgentSettings

getType() - Method in class net.sf.basedb.core.Kit

getType() - Method in class net.sf.basedb.core.Message

getType() - Method in class net.sf.basedb.core.MimeType

getType() - Method in class net.sf.basedb.core.News

getType() - Method in class net.sf.basedb.core.Path

Get the type of the path.

getType() - Method in class net.sf.basedb.core.PermissionTemplate

getType() - Method in class net.sf.basedb.core.PhysicalBioAssay

getType() - Method in class net.sf.basedb.core.Plate

getType() - Method in class net.sf.basedb.core.PlateEvent

getType() - Method in class net.sf.basedb.core.PlateEventType

getType() - Method in class net.sf.basedb.core.PlateGeometry

getType() - Method in class net.sf.basedb.core.PlateMapping

getType() - Method in class net.sf.basedb.core.PlateType

getType() - Method in class net.sf.basedb.core.Platform

getType() - Method in class net.sf.basedb.core.PlatformFileType

getType() - Method in class net.sf.basedb.core.PlatformVariant

getType() - Method in class net.sf.basedb.core.plugin.GuiContext

getType() - Method in class net.sf.basedb.core.PluginConfiguration

getType() - Method in class net.sf.basedb.core.PluginDefinition

getType() - Method in class net.sf.basedb.core.PluginType

getType() - Method in class net.sf.basedb.core.Project

getType() - Method in class net.sf.basedb.core.ProjectKey

getType() - Method in class net.sf.basedb.core.Protocol

getType() - Method in class net.sf.basedb.core.Quantity

getType() - Method in class net.sf.basedb.core.query.QueryParameter

Get the type of the parameter.

getType() - Method in class net.sf.basedb.core.Quota

getType() - Method in class net.sf.basedb.core.QuotaType

getType() - Method in class net.sf.basedb.core.RawBioAssay

getType() - Method in class net.sf.basedb.core.RawDataBatcher

getType() - Method in class net.sf.basedb.core.ReporterBatcher

getType() - Method in class net.sf.basedb.core.ReporterCloneTemplate

getType() - Method in class net.sf.basedb.core.ReporterList

getType() - Method in class net.sf.basedb.core.ReporterType

Get the type of item represented by the object.

getType() - Method in class net.sf.basedb.core.Role

getType() - Method in class net.sf.basedb.core.RoleKey

getType() - Method in class net.sf.basedb.core.RootRawBioAssay

getType() - Method in class net.sf.basedb.core.Sample

getType() - Method in class net.sf.basedb.core.Session

getType() - Method in class net.sf.basedb.core.Software

getType() - Method in class net.sf.basedb.core.SyncFilter

getType() - Method in class net.sf.basedb.core.Tag

getType() - Method in class net.sf.basedb.core.Transformation

getType() - Method in class net.sf.basedb.core.Unit

getType() - Method in class net.sf.basedb.core.User

getType() - Method in class net.sf.basedb.core.UserClientSetting

getType() - Method in class net.sf.basedb.core.UserDefaultSetting

getType() - Method in class net.sf.basedb.core.UserDevice

getType() - Method in class net.sf.basedb.core.VirtualDb

getType() - Method in class net.sf.basedb.core.Well

getType() - Method in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter

getType() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField

getType() - Method in class net.sf.basedb.plugins.executor.ParameterDefinition

Get the type of the parameter.

getType() - Method in class net.sf.basedb.util.export.spotdata.AnnotationAssayField

Return the value type of the annotation type, or null if not configured.

getType() - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField

getType() - Method in interface net.sf.basedb.util.export.spotdata.ExportableField

Get the data type of the field.

getType() - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField

getType() - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField

getType() - Method in class net.sf.basedb.util.extensions.xml.PluginInfo

Get the main type of the plug-in.

getTypeCode() - Method in class net.sf.basedb.clients.web.taglib.Page

getTypeFormatter(SessionControl, Type) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory

Get a formattater that is encoding strings for HTML output.

getTypeFormatter(SessionControl, Type, boolean) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory

Get a formatter suitable for displaying values of the given type.

getTypeHelper() - Method in class net.sf.basedb.core.hibernate.SessionWrapper

getTypes() - Method in class net.sf.basedb.core.log.EntityDetails

Get an array representing the data type for each property.

getTypeWrapper() - Method in enum class net.sf.basedb.core.Type

Get a wrapper for accessing underlying type information from Hibernate.

getTypeWrapper() - Method in class net.sf.basedb.core.VirtualColumn

Get a wrapper for accessing underlying type information from Hibernate.

getUniqueKeys() - Method in class net.sf.basedb.util.bfs.MetadataWriter

Checks if the current section requires entry names to be unique or not.

getUnit() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

getUnit() - Method in class net.sf.basedb.core.Annotation

Get the unit used for the values in this annotation.

getUnit() - Method in class net.sf.basedb.core.data.AnnotationData

Get the unit used for the annotation values.

getUnit() - Method in class net.sf.basedb.core.data.PropertyFilterData

getUnit() - Method in class net.sf.basedb.core.data.UnitSymbolData

Get the unit this symbol belongs to.

getUnit() - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil

Get the unit of the last annotation values that was found by AnnotationLoaderUtil.find(AnnotationSetSnapshot).

getUnit(String) - Method in class net.sf.basedb.core.Quantity

Get a a unit by symbol, also checking among the aliases.

getUnit(DbControl, String, String) - Static method in class net.sf.basedb.util.units.UnitUtil

Find the unit with a given symbol for a given quantity.

getUnit(Session, String) - Method in class net.sf.basedb.core.Quantity

Get the unit with a given symbol, or null if no unit is found.

getUnitConverter(Unit) - Method in class net.sf.basedb.core.Annotation

Get a converter for converting the values in this annotation to a specific unit.

getUnitConverter(Unit) - Method in class net.sf.basedb.core.Unit

Create a unit converter for converting from the reference unit (other) to this unit.

getUnitConverter(Unit, Unit) - Method in class net.sf.basedb.core.AnnotationBatcher

Get/create a unit converter for converting between two units.

getUnitFormatter(Formatter<T>, Unit) - Method in class net.sf.basedb.core.Annotation

Wrap a parent formatter with a formatter for units.

getUnitId() - Method in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo

Get the ID of the unit this annotation is using.

getUnits() - Method in class net.sf.basedb.core.data.QuantityData

This is the inverse end.

getUnits() - Method in class net.sf.basedb.core.Quantity

Get a query that returns all units of this quantity.

getUnitSymbol() - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil

Get the unit symbol of the last annotation values that was found by AnnotationLoaderUtil.find(AnnotationSetSnapshot).

getUnitSymbol(Unit) - Method in class net.sf.basedb.core.Annotation

Shortcut for Unit.getDisplaySymbol(), but also checks the default unit of the annotation type.

getUnknownLines() - Method in class net.sf.basedb.util.parser.FlatFileParser

Get the number of lines that the last call to FlatFileParser.nextData() or FlatFileParser.hasMoreData() ignored because they couldn't be interpreted as data lines.

getUnpackDirectory(DbControl) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker

Get the directory where the unpacked files are placed by the plugin.

getUnselectedtext() - Method in class net.sf.basedb.clients.web.taglib.Select

getUnverifiedDeviceInfo() - Method in class net.sf.basedb.core.SessionControl

Get information about a device that is currently waiting to be verified.

getUpdatePropertyOrder(Class<? extends BatchableData>) - Static method in class net.sf.basedb.core.BatchUtil

Get the order of properties in the update SQL.

getUpdatePropertyOrder(String) - Static method in class net.sf.basedb.core.BatchUtil

Get the order of properties in the update SQL.

getUpdateSql(Class<? extends BatchableData>) - Static method in class net.sf.basedb.core.BatchUtil

Get the SQL that updates a new row of the specified class.

getUpdateSql(String) - Static method in class net.sf.basedb.core.BatchUtil

Get the SQL that updates a new row of the specified class.

getUploadStream(boolean) - Method in class net.sf.basedb.core.File

Get an OutputStream that can be used to upload a physical file for this file item.

getUploadStream(boolean, Boolean) - Method in class net.sf.basedb.core.File

Get an OutputStream that can be used to upload a physical file for this file item.

getUpperLimit() - Method in class net.sf.basedb.core.DoubleParameterType

Get the highest valid value of the parameter.

getUpperLimit() - Method in class net.sf.basedb.core.FloatParameterType

Get the highest valid value of the parameter.

getUpperLimit() - Method in class net.sf.basedb.core.IntegerParameterType

Get the highest valid value of the parameter.

getUpperLimit() - Method in class net.sf.basedb.core.LongParameterType

Get the highest valid value of the parameter.

getURI() - Method in class net.sf.basedb.core.File

Get the URL of an external file as an URI.

getURI() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile

Get an URI that points to the extensions file.

getURI() - Method in interface net.sf.basedb.util.uri.ConnectionManager

Get the URI of the resource we are interested in.

getURI() - Method in class net.sf.basedb.util.uri.http.HttpConnectionManager

getUrl() - Method in interface net.sf.basedb.clients.web.extensions.plot.PlotGenerator

Get the URL to a servlet that is used to generate the image.

getUrl() - Method in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean

getUrl() - Method in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory

getUrl() - Method in interface net.sf.basedb.clients.web.extensions.startpage.StartPageAction

Get the URL to the start page.

getUrl() - Method in class net.sf.basedb.clients.web.extensions.startpage.StartPageBean

getUrl() - Method in class net.sf.basedb.core.authentication.ExtraUserInformation

An URL to the user homepage (or similar).

getUrl() - Method in class net.sf.basedb.core.data.FileData

Get the URL to the file.

getUrl() - Method in class net.sf.basedb.core.data.PluginDefinitionData

Get a URL with more information about the plugin.

getUrl() - Method in class net.sf.basedb.core.data.UserData

Get the URL to the user's homepage, or null if unknown.

getUrl() - Method in class net.sf.basedb.core.File

Get the URL to the (external) file.

getUrl() - Method in interface net.sf.basedb.core.plugin.About

An URL to get more information about the plugin.

getUrl() - Method in class net.sf.basedb.core.plugin.AboutImpl

getUrl() - Method in class net.sf.basedb.core.PluginDefinition

Get a URL with more information about the plugin.

getUrl() - Method in class net.sf.basedb.core.User

Get the URL to the user's homepage.

getUrl() - Method in class net.sf.basedb.util.extensions.AboutBean

getUrl() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout

getUrl(Object) - Method in class net.sf.basedb.core.ExtendedProperty

Create a link for this extended property.

getUrl(Object) - Method in class net.sf.basedb.core.ExtendedPropertyLinker

Create a link.

getURLToMap(Float, Float) - Static method in class net.sf.basedb.util.GeoLocation

Get an URL that opens a map marking the given position.

getUsableUnits() - Method in class net.sf.basedb.core.AnnotationType

Get a query for returning the units that are considered "usable" for this annotation type.

getUsableUnits() - Method in class net.sf.basedb.core.data.AnnotationTypeData

The units that it makes sense to use with this annotation type.

getUseDeviceVerification() - Method in class net.sf.basedb.core.data.UserData

A flag indicating if this user want to use device verification.

getUseDeviceVerification() - Method in class net.sf.basedb.core.User

A flag indicating if device verification has been enabled for this account.

getUsedMemory() - Method in class net.sf.basedb.core.JobAgent

Get the current memory usage in bytes of the server where the job agent is running.

getUsedMemory() - Method in class net.sf.basedb.util.jobagent.JobAgentInfo

Get the used memory on the job agent's server in bytes.

getUsedQuantity() - Method in class net.sf.basedb.core.BioMaterialEvent

Get the quantity that was used from the biomaterial by this event.

getUsedQuantity() - Method in class net.sf.basedb.core.BioMaterialEventSource

Get the quantity that was used from the source biomaterial by the event.

getUsedQuantity() - Method in class net.sf.basedb.core.data.BioMaterialEventData

Get the used quantity of the biomaterial affected by this event.

getUsedQuantity() - Method in class net.sf.basedb.core.data.BioMaterialEventSourceData

Get the used quantity from the parent biomaterial.

getUsedQuantity(MeasuredBioMaterial) - Method in class net.sf.basedb.core.BioMaterialEvent

Get the quantity that was used by this event for the specified biomaterial.

getUsedQuantity(FlatFileParser.Data, BioMaterialEventSource) - Method in class net.sf.basedb.plugins.batchimport.UsedQuantityMapper

Get the used quantity from the parent item.

getUsedSlot() - Method in class net.sf.basedb.core.InternalJobQueue.JobRunner

The slot the job is executing in.

getUsedUnits() - Method in class net.sf.basedb.core.data.UnitData

This is the inverse end.

getUsedWells() - Method in class net.sf.basedb.core.BioPlate

Get the number of used wells on this plate.

getUseInternalJobQueue() - Method in class net.sf.basedb.core.data.PluginDefinitionData

If the plug-in can be executed with the internal job queue or not.

getUseInternalJobQueue() - Method in class net.sf.basedb.core.PluginDefinition

If this plug-in can be executed by the internal job queue or not.

getUseNullIfException() - Method in class net.sf.basedb.util.parser.FlatFileParser

getUsePermissions() - Method in class net.sf.basedb.core.data.PluginDefinitionData

If the permissions for this plugin should be used or not.

getUsePermissions() - Method in class net.sf.basedb.core.PluginDefinition

Check if this plugin should execute with or without permissions.

getUser() - Method in class net.sf.basedb.core.BioMaterialEvent

Get the User that is responsible for this event.

getUser() - Method in class net.sf.basedb.core.data.BioMaterialEventData

Get the user that is responsible for this event, typically this is the user that entered the information in the database.

getUser() - Method in class net.sf.basedb.core.data.ChangeHistoryData

getUser() - Method in class net.sf.basedb.core.data.ContextData

Get the user that owns this context.

getUser() - Method in class net.sf.basedb.core.data.DiskUsageData

Get the user that owns the DiskConsumable item.

getUser() - Method in class net.sf.basedb.core.data.PasswordData

Get the user this password is referring to.

getUser() - Method in class net.sf.basedb.core.data.PlateEventData

Get the user that is responsible for this event, typically this is the user that entered the information in the database.

getUser() - Method in class net.sf.basedb.core.data.SessionData

Get the user that logged in with this session.

getUser() - Method in class net.sf.basedb.core.data.UserClientSettingData

Get the user this setting is valid for.

getUser() - Method in class net.sf.basedb.core.data.UserDefaultSettingData

Get the user this setting is valid for.

getUser() - Method in class net.sf.basedb.core.data.UserDeviceData

The user that this device is associated with.

getUser() - Method in class net.sf.basedb.core.DiskUsage

Get the user that owns the DiskConsumable item.

getUser() - Method in class net.sf.basedb.core.PlateEvent

Get the User that is responsible for this event.

getUser() - Method in class net.sf.basedb.core.Session

Get the user that logged in with this session.

getUser() - Method in class net.sf.basedb.core.UserClientSetting

Get the user this setting is valid for.

getUser() - Method in class net.sf.basedb.core.UserDefaultSetting

Get the user this setting is valid for.

getUser() - Method in class net.sf.basedb.core.UserDevice

Get the user that owns this device.

getUser(DbControl) - Method in class net.sf.basedb.core.ChangeHistory

Load the user that made the change.

getUser(DbControl) - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo

Load the user that made the change.

getUser(DbControl, ChangeHistory, boolean, boolean) - Static method in class net.sf.basedb.clients.web.ChangeHistoryUtil

Get the user that made the change in HTML format.

getUserAgent() - Method in class net.sf.basedb.core.data.UserDeviceData

Get a string with more information about the device (eg.

getUserAgent() - Method in class net.sf.basedb.core.UserDevice

Get the user agent string of this device.

getUserByExternalId(String) - Method in class net.sf.basedb.core.AuthenticationContext

Load a user item from the BASE database given an external id.

getUserById(int) - Method in class net.sf.basedb.core.AuthenticationContext

Load a user item from the BASE database given an internal id.

getUserByLogin(String) - Method in class net.sf.basedb.core.AuthenticationContext

Load a user item from the BASE database given a login name.

getUserClientSetting(String) - Method in class net.sf.basedb.core.SessionControl

Get the value of the UserClientSetting with the specified name.

getUserDefaultSetting(String) - Method in class net.sf.basedb.core.SessionControl

Get the value of the UserDefaultSetting with the specified name.

getUserEmail() - Method in class net.sf.basedb.core.SessionControl.UnverifiedDeviceInfo

Get the email to the user.

getUserFilesDirectory() - Static method in class net.sf.basedb.core.Application

Get the path to the directory where uploaded files are stored.

getUserId() - Method in class net.sf.basedb.core.authentication.LoginRequest

Get the user id to use.

getUserId() - Method in class net.sf.basedb.core.ChangeHistory

Get the ID of the user that made the change.

getUserId() - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo

Get the ID of the user that executed the transaction.

getUserId() - Method in class net.sf.basedb.core.data.ChangeHistoryData

The ID of the user that made the change.

getUserId() - Method in class net.sf.basedb.core.data.keyring.UserGroups

Get the id of the user.

getUserId() - Method in class net.sf.basedb.core.data.keyring.UserKeys

Get the id of the user.

getUserId() - Method in class net.sf.basedb.core.data.keyring.UserProjects

Get the id of the user.

getUserId() - Method in class net.sf.basedb.core.data.keyring.UserRoles

Get the id of the user.

getUserId() - Method in class net.sf.basedb.core.log.TransactionDetails

Get the ID of the currently logged in user, or 0 if no user is logged in.

getUserIds(Permission) - Method in class net.sf.basedb.core.ItemKey

Get the ID:s of all users that have the specified permission in this item key.

getUserLogin() - Method in class net.sf.basedb.core.Path

Get the userlogin part of the path.

getUsername() - Method in class net.sf.basedb.core.data.FileServerData

Get the username that is used to login to the server.

getUsername() - Method in class net.sf.basedb.core.FileServer

Get the username that is required to authenticate with the file server.

getUsername() - Method in class net.sf.basedb.util.uri.ConnectionParameters

Get the username that should be used to authenticate the user.

getUserName() - Method in class net.sf.basedb.core.log.TransactionDetails

Utility method for loading the name of the currently logged in user.

getUserName() - Method in class net.sf.basedb.core.SessionControl.UnverifiedDeviceInfo

Get the name of the user.

getUserPermissions() - Method in class net.sf.basedb.core.UserPermissions

Get the internal representation of the permissions.

getUsers() - Method in class net.sf.basedb.core.data.GroupData

Get the set that manages which users are members of this group.

getUsers() - Method in class net.sf.basedb.core.data.ItemKeyData

Get the map that manages which users that have permissions for this key.

getUsers() - Method in class net.sf.basedb.core.data.ProjectData

Get the map that manages which users are members of this project and their permissions.

getUsers() - Method in class net.sf.basedb.core.data.RoleData

Get the set that manages which users are members of this role.

getUsers() - Method in class net.sf.basedb.core.Group

Get a query that returns the users that are members of this group.

getUsers() - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring

Return empty set.

getUsers() - Method in class net.sf.basedb.core.Job.SignalKeyring

Return empty set.

getUsers() - Method in class net.sf.basedb.core.Keyring

Get all users that share group membership with the logged in user.

getUsers() - Method in class net.sf.basedb.core.MultiPermissions

Get a query that returns all users appearing in at least one of the item keys.

getUsers() - Method in class net.sf.basedb.core.Project

Get a query that returns the users that are members of this project.

getUsers() - Method in class net.sf.basedb.core.Role

Get a query that returns the users that are members of this role.

getUsers() - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring

Return empty set.

getUserSettings() - Method in class net.sf.basedb.core.data.ClientData

This is the inverse end.

getUsingItems() - Method in class net.sf.basedb.core.AnnotationSet

Get the item this annotation set belongs to.

getUsingItems() - Method in class net.sf.basedb.core.AnnotationType

Get all: Annotations of this type Experiments that are using this annotation type as an experimental factor Protocols that are using this annotation type as a protocol parameter

getUsingItems() - Method in class net.sf.basedb.core.ArrayBatch

Get all: ArraySlide:s in this batch

getUsingItems() - Method in class net.sf.basedb.core.ArrayDesign

Get all: ArrayBatch:s of this design RawBioAssay:s of this design

getUsingItems() - Method in class net.sf.basedb.core.ArrayDesignBlock

Get the array design this block is a part of.

getUsingItems() - Method in class net.sf.basedb.core.ArrayDesignPlate

Get the array design this plate is used on.

getUsingItems() - Method in class net.sf.basedb.core.ArraySlide

Get the bioassay that was used on this plate.

getUsingItems() - Method in class net.sf.basedb.core.BasicItem

Get all items that are using this item.

getUsingItems() - Method in class net.sf.basedb.core.BioPlate

Gets all MeasuredBioMaterial located on this plate and all child plates created from this plate.

getUsingItems() - Method in class net.sf.basedb.core.BioPlateEventType

Gets all BioPlates and BioPlateEventDefinitions using this type

getUsingItems() - Method in class net.sf.basedb.core.BioPlateType

Gets all BioPlates and BioPlateEventDefinitions using this type

getUsingItems() - Method in class net.sf.basedb.core.BioSource

Get all: Sample:s created from this biosource

getUsingItems() - Method in class net.sf.basedb.core.BioWell

Adds the MeasuredBioMaterial,used in this well, to the Set.

getUsingItems() - Method in class net.sf.basedb.core.DataFileType

Get all: FileSetMember:s using this file type Platform:s using this file type ItemSubtype:s using this file type

getUsingItems() - Method in class net.sf.basedb.core.DerivedBioAssay

Get all: Child derived bioassays Child raw bioassays

getUsingItems() - Method in class net.sf.basedb.core.Directory

Get all: File:s in this directory Sub-Directory:s in this directory User:s having this directory as their home-directory Experiment:s having this directory as the plugin directory

getUsingItems() - Method in class net.sf.basedb.core.DiskUsage

Get the item this disk usage information belongs to.

getUsingItems() - Method in class net.sf.basedb.core.Extract

Get all: Child extracts created from the extract PhysicalBioAssay:s created from this extract DerivedBioAssay:s referencing the extract RawBioAssay:s referencing the extract

getUsingItems() - Method in class net.sf.basedb.core.ExtraValueType

Get all: ExtraValue:s of this type

getUsingItems() - Method in class net.sf.basedb.core.File

Get all: FileAttachable items with this file attached

getUsingItems() - Method in class net.sf.basedb.core.FileServer

Get all files registered with this server.

getUsingItems() - Method in class net.sf.basedb.core.FileSet

Get the item this file set belongs to.

getUsingItems() - Method in class net.sf.basedb.core.Group

Get all: User:s assigned to this group as a quota group

getUsingItems() - Method in class net.sf.basedb.core.Hardware

Get all: DerivedBioAssay:s with this hardware ArrayBatch:s with this hardware BioMaterial:s and PhysicalBioAssay:s with this hardware Plate:s with this hardware

getUsingItems() - Method in class net.sf.basedb.core.ItemKey

Get all: Shareable items shared to this key

getUsingItems() - Method in class net.sf.basedb.core.ItemSubtype

Get all: Subtypable items of this subtype.

getUsingItems() - Method in class net.sf.basedb.core.Job

Get the transformation and raw bioassays using this job.

getUsingItems() - Method in class net.sf.basedb.core.Kit

Get all: BioMaterial:s and PhysicalBioAssay:s using this kit BioPlateEvent:s with this kit DerivedBioAssay: with this kit

getUsingItems() - Method in class net.sf.basedb.core.MeasuredBioMaterial

Get all: BioMaterial:s where this item has been used as a source

getUsingItems() - Method in class net.sf.basedb.core.PermissionTemplate

Get all: Project:s using this permission template

getUsingItems() - Method in class net.sf.basedb.core.PhysicalBioAssay

Get all: (root) DerivedBioAssay:s created from this physical bioassay

getUsingItems() - Method in class net.sf.basedb.core.Plate

Get all: Child plates ArrayDesign:s using this plate

getUsingItems() - Method in class net.sf.basedb.core.PlateEventType

Get all: PlateEvent:s of this type

getUsingItems() - Method in class net.sf.basedb.core.PlateGeometry

Get all: PlateType:s of this geometry PlateMapping:s using this geometry BioPlate:s using this geometry

getUsingItems() - Method in class net.sf.basedb.core.PlateMapping

Get all: Plate:s created with this mapping

getUsingItems() - Method in class net.sf.basedb.core.PlateType

Get all: Plate:s created from this plate type

getUsingItems() - Method in class net.sf.basedb.core.Platform

Get all: ArrayDesign:s and RawBioAssay:s using this platform

getUsingItems() - Method in class net.sf.basedb.core.PlatformVariant

Get all: ArrayDesign:s and RawBioAssay:s using this platform variant

getUsingItems() - Method in class net.sf.basedb.core.PluginConfiguration

Get all: Job:s using this configuration

getUsingItems() - Method in class net.sf.basedb.core.PluginDefinition

Get all: PluginConfiguration:s created from this plugin Job:s using this plugin

getUsingItems() - Method in class net.sf.basedb.core.ProjectKey

Get all: Shareable items shared to this key

getUsingItems() - Method in class net.sf.basedb.core.Protocol

Get all: a BioMaterial:s and PhysicalBioAssay:s using this protocol a Plate:s using this protocol an ArrayBatch:s using this protocol a DerivedBioAssay:s using this protocol a RawBioAssay:s using this protocol

getUsingItems() - Method in class net.sf.basedb.core.Quantity

Get all: Unit:s for this quantity AnnotationType:s using this quantity

getUsingItems() - Method in class net.sf.basedb.core.Quota

Get all: User:s assigned to this quota Group:s assigned to this quota

getUsingItems() - Method in class net.sf.basedb.core.RawBioAssay

Get all: Experiment:s using this raw bioassay Transformation:s using this raw bioassay

getUsingItems() - Method in class net.sf.basedb.core.ReporterCloneTemplate

Get all: Experiment that is using this template

getUsingItems() - Method in class net.sf.basedb.core.ReporterType

Get all: Reporter:s of this type

getUsingItems() - Method in class net.sf.basedb.core.Sample

Get all: Extract:s created from this sample Pooled samples

getUsingItems() - Method in class net.sf.basedb.core.Software

Get all: RawBioAssay:s created with this software DerivedBioAssay: created with this software

getUsingItems() - Method in class net.sf.basedb.core.Tag

Get all: Extract:s marked with this tag

getUsingItems() - Method in class net.sf.basedb.core.Unit

Get all: AnnotationType:s using this unit as default unit Annotation:s using this unit

getUsingItems() - Method in class net.sf.basedb.core.User

Get all: Ownable items owned by this user

getUsingItems() - Method in class net.sf.basedb.core.Well

Get all: Child wells Features derived from this well

getValidatedXml(String, URL) - Static method in class net.sf.basedb.util.XmlUtil2

getValidatedXml(URL, URL) - Static method in class net.sf.basedb.util.XmlUtil2

Load and validate an XML file against a DTD, and return it as a Document object.

getValidatedXML(InputStream, URL, String) - Static method in class net.sf.basedb.util.XmlUtil2

Validate an InputStream against a DTD file and return it as a Document

getValidationError() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile

Get more information about the error that caused the validation to fail.

getValidationOptions() - Method in class net.sf.basedb.util.overview.GenericOverview

Get the validation options currently in use.

getValidationOptions() - Method in interface net.sf.basedb.util.overview.OverviewContext

Get the validation options that are currently in effect.

getValidationPresets(SessionControl) - Static method in class net.sf.basedb.util.overview.OverviewUtil

Get the validation options presets for the currently logged in user.

getValidationRule(InvokationContext<? super ValidationRuleAction>) - Method in class net.sf.basedb.util.overview.extensions.ReflectValidationRuleActionFactory

getValidator() - Method in class net.sf.basedb.util.overview.Failure

Get the validation rule that failed.

getValidators(DbControl) - Method in class net.sf.basedb.util.overview.validator.ExtensionNodeValidator

getValue() - Method in class net.sf.basedb.clients.web.extensions.DynamicActionAttribute

Get the value of the dynamic attribute.

getValue() - Method in class net.sf.basedb.clients.web.taglib.Input

getValue() - Method in class net.sf.basedb.clients.web.taglib.table.Cell

getValue() - Method in class net.sf.basedb.clients.web.taglib.table.CellValue

getValue() - Method in class net.sf.basedb.clients.web.taglib.table.Hidden

getValue() - Method in enum class net.sf.basedb.core.BioMaterialEvent.Type

Get the integer value that is used when storing a BioMaterialEvent.Type to the database.

getValue() - Method in enum class net.sf.basedb.core.BioWell.LockMode

Get the integer value that is used when storing a lock mode to the database.

getValue() - Method in class net.sf.basedb.core.data.PropertyFilterData

Get the value used in this filter.

getValue() - Method in class net.sf.basedb.core.data.SettingData

Get the value of this setting.

getValue() - Method in enum class net.sf.basedb.core.ExtraValue.CoordinateType

Get the integer value that is used when storing a CoordinateType in the database.

getValue() - Method in enum class net.sf.basedb.core.FeatureIdentificationMethod

Get the integer value that is used when storing the feature identification method to the database.

getValue() - Method in enum class net.sf.basedb.core.Formula.AverageMethod

Get the integer value that is used when storing a Formula.AverageMethod in the database.

getValue() - Method in enum class net.sf.basedb.core.Formula.Parser

Get the integer value that is used when storing a Formula.Parser in the database.

getValue() - Method in enum class net.sf.basedb.core.Formula.Type

Get the integer value that is used when storing a Formula.Type in the database.

getValue() - Method in enum class net.sf.basedb.core.Include

getValue() - Method in enum class net.sf.basedb.core.IntensityTransform

Get the integer value that is used when storing a transform in the database.

getValue() - Method in enum class net.sf.basedb.core.Item

Get the integer value that is used when storing an item to the database.

getValue() - Method in enum class net.sf.basedb.core.ItemContext.SortDirection

Get the integer value that is used when storing an location to the database.

getValue() - Method in enum class net.sf.basedb.core.Job.ExecutionTime

Get the integer value that is used when storing a Job.ExecutionTime in the database.

getValue() - Method in enum class net.sf.basedb.core.Job.Status

Get the integer value that is used when storing a Job.Status to the database.

getValue() - Method in enum class net.sf.basedb.core.Job.Type

Get the integer value that is used when storing a Job.Status to the database.

getValue() - Method in enum class net.sf.basedb.core.Location

Get the integer value that is used when storing an location to the database.

getValue() - Method in enum class net.sf.basedb.core.log.ChangeType

Get the numerical value for this change type.

getValue() - Method in enum class net.sf.basedb.core.Operator

Get the integer value that is used when storing an operator in the database.

getValue() - Method in enum class net.sf.basedb.core.plugin.GuiContext.Type

Get the integer value that is used when storing a GuiContext.Type to the database.

getValue() - Method in enum class net.sf.basedb.core.plugin.Plugin.MainType

getValue() - Method in class net.sf.basedb.core.PropertyFilter

Get the value to use in the filter.

getValue() - Method in class net.sf.basedb.core.query.QueryParameter

Get the value of the parameter.

getValue() - Method in class net.sf.basedb.core.query.WhenStatement

Get the value returned by this statement

getValue() - Method in class net.sf.basedb.core.Setting

Get the value of this setting.

getValue() - Method in enum class net.sf.basedb.core.Type

Get the integer value that is used when storing a type in the database.

getValue() - Method in class net.sf.basedb.util.bfs.MetadataModel.SectionEntry

Get the value of the entry.

getValue() - Method in class net.sf.basedb.util.Enumeration.Entry

getValue() - Method in class net.sf.basedb.util.excel.ExcelValue

Get the stored value.

getValue() - Method in class net.sf.basedb.util.fuzzy.StringMatcher.FuzzyMatch

Get the value string.

getValue(int) - Method in class net.sf.basedb.util.bfs.MetadataModel.Section

Get the value of the entry at the given index.

getValue(int) - Method in class net.sf.basedb.util.Enumeration

getValue(String) - Method in class net.sf.basedb.core.ParameterValuesImpl

getValue(String) - Method in class net.sf.basedb.core.plugin.NamespaceParameterValuesWrapper

getValue(String) - Method in interface net.sf.basedb.core.plugin.ParameterValues

Get a single value for a specific parameter.

getValue(String) - Method in class net.sf.basedb.core.plugin.ParameterValuesWrapper

Get the value of the parameter with the specified name.

getValue(String) - Method in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues

getValue(String) - Method in class net.sf.basedb.util.bfs.MetadataModel.Section

Get the value of the first entry with a given key.

getValue(String) - Method in class net.sf.basedb.util.QueryParameters

Get the (single) value for a key.

getValue(String, String) - Method in class net.sf.basedb.util.bfs.MetadataModel

Utility method for getting the value of the first entry in the first section that matches the given section and key name.

getValue(Map<String, List<String>>, String) - Method in class net.sf.basedb.util.jobagent.JobAgentInfo

getValue(Map<String, List<String>>, String) - Method in class net.sf.basedb.util.jobagent.JobInfo

getValue(RelatedItemHelper, Annotatable, SourceItemTransformer) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemAnnotationColumn

getValue(RelatedItemHelper, Annotatable, SourceItemTransformer) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn

Alternate implementation for loading data.

getValue(RelatedItemHelper, Annotatable, SourceItemTransformer) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemErrorColumn

getValue(RelatedItemHelper, Annotatable, SourceItemTransformer) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemExtensionColumn

getValue(RelatedItemHelper, Annotatable, SourceItemTransformer) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemListColumn

getValue(RelatedItemHelper, Annotatable, SourceItemTransformer) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemMultiHopColumn

getValue(RelatedItemHelper, Annotatable, SourceItemTransformer) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemPropertyColumn

getValue(DbControl, C) - Method in class net.sf.basedb.core.Metadata.BasicData2ItemPropertyPath

getValue(DbControl, C) - Method in class net.sf.basedb.core.Metadata.BasicItem2DataPropertyPath

getValue(DbControl, C) - Method in class net.sf.basedb.core.Metadata.CombinedPropertyPath

getValue(DbControl, C) - Method in class net.sf.basedb.core.Metadata.ComponentPropertyPath

getValue(DbControl, C) - Method in class net.sf.basedb.core.Metadata.EntityPropertyPath

getValue(DbControl, C) - Method in class net.sf.basedb.core.Metadata.EvictPropertyPath

getValue(DbControl, C) - Method in class net.sf.basedb.core.Metadata.NoopPropertyPath

getValue(DbControl, C) - Method in interface net.sf.basedb.core.Metadata.PropertyPath

Get the value as defined by the implementation for the given item.

getValue(DbControl, I) - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction

Get the value that should be displayed in the column.

getValue(DbControl, I) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory.PropertyPathAction

getValue(DbControl, Collection<C>) - Method in class net.sf.basedb.core.Metadata.CollectionPropertyPath

getValue(DbControl, Date) - Method in class net.sf.basedb.core.Metadata.DateCopyPropertyPath

getValue(DbControl, Map) - Method in class net.sf.basedb.core.Metadata.MapPropertyPath

getValue(DbControl, Annotatable) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn

We finalize this implementation to make sure that the helper implementation always get a chance to re-cycle transactions.

getValue(DbControl, BasicItem) - Method in class net.sf.basedb.clients.web.extensions.list.AnyLinkColumn

getValue(DbControl, IdentifiableData) - Method in class net.sf.basedb.core.Metadata.IdentifierPropertyPath

getValue(DbControl, ReporterScore) - Method in class net.sf.basedb.core.Metadata.ReporterScore2DataPropertyPath

getValue(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.ColumnMapper

Deprecated.

getValue(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.CompoundMapper

Deprecated.

getValue(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.ConstantMapper

Deprecated.

getValue(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.CropStringMapper

Deprecated.

getValue(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.JepMapper

Deprecated.

getValue(FlatFileParser.Data) - Method in interface net.sf.basedb.util.parser.Mapper

Deprecated.

In 3.15, use Mapper.getString(FlatFileParser.Data) instead or one of the other getXxxx() methods to get a given data type directly

getValue(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.NullIfExceptionMapper

Deprecated.

getValue(FlatFileParser.Data, int) - Method in class net.sf.basedb.util.importer.spotdata.ExtraFloatParser

Get the extra value from the data.

getValue(T, T, T) - Method in class net.sf.basedb.util.Diff3

Get the correct value to set on the newItem object.

getValueAsObject() - Method in class net.sf.basedb.core.PropertyFilter

Get the value as an object of the correct type.

getValueAsObject() - Method in class net.sf.basedb.util.jep.FunctionSafeJep

Override the superclass method so that exceptions are passed on instead of swallowed.

getValueAsObject(String, Unit, boolean) - Method in class net.sf.basedb.core.PropertyFilter

getValueAsObject(Unit, boolean) - Method in class net.sf.basedb.core.PropertyFilter

Get the value as an object of the proper type converted to the specified unit.

getValueClass() - Method in enum class net.sf.basedb.core.Type

Get the class of objects that can be used as values for this type.

getValueCount() - Method in class net.sf.basedb.util.bfs.MetadataModel.SectionEntry

Get the number of values in the entry.

getValueCount() - Method in class net.sf.basedb.util.bfs.MetadataWriter

Get the number of values that has been written to the current section so far.

getValueId() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink

getValueList2(Element, Class<T>) - Method in class net.sf.basedb.core.PluginConfiguration

Gets the list of values for a parameter from the XML-file.

getValues() - Method in class net.sf.basedb.core.Annotation

Get the values this annotation contains.

getValues() - Method in class net.sf.basedb.core.AnnotationType

Get the list of allowed values if this annotation type is an enumeration.

getValues() - Method in class net.sf.basedb.core.data.AnnotationData

The values of this annotation.

getValues() - Method in class net.sf.basedb.core.data.BooleanParameterValueData

getValues() - Method in class net.sf.basedb.core.data.DateParameterValueData

getValues() - Method in class net.sf.basedb.core.data.DoubleParameterValueData

getValues() - Method in class net.sf.basedb.core.data.FloatParameterValueData

getValues() - Method in class net.sf.basedb.core.data.IntegerParameterValueData

getValues() - Method in class net.sf.basedb.core.data.ItemParameterValueData

getValues() - Method in class net.sf.basedb.core.data.LongParameterValueData

getValues() - Method in class net.sf.basedb.core.data.ParameterValueData

Get values of this parameter.

getValues() - Method in class net.sf.basedb.core.data.StringParameterValueData

getValues() - Method in class net.sf.basedb.core.data.TextParameterValueData

getValues() - Method in class net.sf.basedb.core.data.TimestampParameterValueData

getValues() - Method in class net.sf.basedb.core.ExtraValue

Get a query returning the extra values.

getValues() - Method in class net.sf.basedb.core.ParameterInfo

getValues() - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil

Get the values from the last annotation found when calling AnnotationLoaderUtil.find(AnnotationSetSnapshot)

getValues() - Method in class net.sf.basedb.plugins.executor.ProgramParameter

Get the values for this parameter.

getValues() - Method in class net.sf.basedb.util.bfs.MetadataModel.SectionEntry

Get all values.

getValues() - Method in class net.sf.basedb.util.plot.PlotAnnotation

The values that falls into this annotation.

getValues(int) - Method in class net.sf.basedb.util.bfs.MetadataModel.Section

Get the values of the entry at the given index.

getValues(String) - Method in class net.sf.basedb.core.ParameterValuesImpl

getValues(String) - Method in class net.sf.basedb.core.plugin.NamespaceParameterValuesWrapper

getValues(String) - Method in interface net.sf.basedb.core.plugin.ParameterValues

Get a List of values for a specific parameter.

getValues(String) - Method in class net.sf.basedb.core.plugin.ParameterValuesWrapper

Get the values of the parameter with the specified name.

getValues(String) - Method in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues

getValues(String) - Method in class net.sf.basedb.util.bfs.MetadataModel.Section

Get the values of the first entry with a given key.

getValues(String) - Method in class net.sf.basedb.util.QueryParameters

Get all values for a key.

getValues(String, String) - Method in class net.sf.basedb.util.bfs.MetadataModel

Utility method for getting the values of the first entry in the first section that matches the given section and key name.

getValues(Map<String, List<String>>, String) - Method in class net.sf.basedb.util.jobagent.JobAgentInfo

getValues(Unit) - Method in class net.sf.basedb.core.Annotation

Get the values for this annotation in a specific unit.

getValuesAsObjects() - Method in class net.sf.basedb.core.PropertyFilter

Splits the value string at each "|" and creates a list with objects from the substrings that were found.

getValuesAsObjects(String, Unit, boolean) - Method in class net.sf.basedb.core.PropertyFilter

getValuesAsObjects(Unit, boolean) - Method in class net.sf.basedb.core.PropertyFilter

Same as PropertyFilter.getValueAsObject(Unit, boolean) but the filter string is first split at each "|".

getValueSeparator() - Method in class net.sf.basedb.core.PropertyFilter

getValuesOrMask() - Method in class net.sf.basedb.core.ParameterInfo

Utility method for getting the values or a mask (*****) if the ParameterInfo.isMasked() flag is set.

getValuesOrMask(String) - Method in class net.sf.basedb.core.ParameterInfo

Utility method for getting the values or a mask if the ParameterInfo.isMasked() flag is set.

getValuesVersion() - Method in class net.sf.basedb.core.Annotation

Get the version number of the item keeping the values.

getValueType() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

getValueType() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction

The data type of the values that are referenced by the property.

getValueType() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

getValueType() - Method in class net.sf.basedb.core.Annotation

Get the value type for this annotation type.

getValueType() - Method in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo

Shortcut to AnnotationType.getValueType().

getValueType() - Method in class net.sf.basedb.core.AnnotationType

Get the value type for this annotation type.

getValueType() - Method in class net.sf.basedb.core.data.AnnotationTypeData

The code for the value type.

getValueType() - Method in class net.sf.basedb.core.data.BooleanParameterValueData

getValueType() - Method in class net.sf.basedb.core.data.DataCubeExtraValueData

The type of value, ie. int, float or string.

getValueType() - Method in class net.sf.basedb.core.data.DateParameterValueData

getValueType() - Method in class net.sf.basedb.core.data.DoubleParameterValueData

getValueType() - Method in class net.sf.basedb.core.data.ExtraValueTypeData

The code for the value type.

getValueType() - Method in class net.sf.basedb.core.data.FloatParameterValueData

getValueType() - Method in class net.sf.basedb.core.data.FormulaData

The code for the value type. null = not known or doesn't care.

getValueType() - Method in class net.sf.basedb.core.data.IntegerParameterValueData

getValueType() - Method in class net.sf.basedb.core.data.ItemParameterValueData

getValueType() - Method in class net.sf.basedb.core.data.LongParameterValueData

getValueType() - Method in class net.sf.basedb.core.data.ParameterValueData

Get the type of parameter values that are store in this parameter.

getValueType() - Method in class net.sf.basedb.core.data.PropertyFilterData

Get the type of value user for this filter.

getValueType() - Method in class net.sf.basedb.core.data.ReporterClonePropertyData

The code for the value type.

getValueType() - Method in class net.sf.basedb.core.data.StringParameterValueData

getValueType() - Method in class net.sf.basedb.core.data.TextParameterValueData

getValueType() - Method in class net.sf.basedb.core.data.TimestampParameterValueData

getValueType() - Method in class net.sf.basedb.core.DataCubeExtraValue

Get the value type of the extra values.

getValueType() - Method in class net.sf.basedb.core.ExtraValue

Get the type of values.

getValueType() - Method in class net.sf.basedb.core.ExtraValueType

Get the value type for this extra value type.

getValueType() - Method in class net.sf.basedb.core.Formula

Get the type of values that this formula produces.

getValueType() - Method in enum class net.sf.basedb.core.Formula.Type

Get the type of values that formulas of this type must produce or null if it can be any type of values.

getValueType() - Method in class net.sf.basedb.core.ParameterInfo

Get the matching Type for the values stored in this parameter.

getValueType() - Method in class net.sf.basedb.core.ParameterType

Get the date type of values that can be stored in this parameter.

getValueType() - Method in class net.sf.basedb.core.PropertyFilter

Get the type of the property.

getValueType() - Method in class net.sf.basedb.core.query.ParameterExpression

Get the type of value.

getValueType() - Method in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod

getValueType() - Method in class net.sf.basedb.plugins.batchimport.PropertyIdMethod

getVariable(String) - Method in class net.sf.basedb.util.extensions.xml.VariableConverter

Get the value of a variable.

getVariant() - Method in class net.sf.basedb.core.ArrayDesign

getVariant() - Method in class net.sf.basedb.core.BioAssaySet

getVariant() - Method in class net.sf.basedb.core.data.ArrayDesignData

Get the platform variant this raw bioassay uses, or null.

getVariant() - Method in class net.sf.basedb.core.data.FileTypeIndex

getVariant() - Method in class net.sf.basedb.core.data.PlatformFileTypeData

Get the platform variant or null.

getVariant() - Method in class net.sf.basedb.core.data.RawBioAssayData

Get the platform variant this raw bioassay uses, or null.

getVariant() - Method in class net.sf.basedb.core.DerivedBioAssay

getVariant() - Method in class net.sf.basedb.core.ExtraValue

getVariant() - Method in interface net.sf.basedb.core.FileStoreEnabled

Get the platform variant the item is related to.

getVariant() - Method in class net.sf.basedb.core.PlatformFileType

Get the platform variant.

getVariant() - Method in class net.sf.basedb.core.RawBioAssay

getVariant(DbControl) - Method in class net.sf.basedb.core.RawDataType

Get the platform variant that this raw data type is associated with.

getVariantRawDataType(Session, String) - Static method in class net.sf.basedb.core.RawDataTypes

getVariants() - Method in class net.sf.basedb.core.data.PlatformData

The variants of this platform.

getVariants() - Method in class net.sf.basedb.core.Platform

Get a query that returns variants of this platform.

getVersion() - Method in class net.sf.basedb.core.BasicItem

getVersion() - Method in class net.sf.basedb.core.data.BasicData

Get the version of the item.

getVersion() - Method in interface net.sf.basedb.core.data.IdentifiableData

Get the version of this item.

getVersion() - Method in class net.sf.basedb.core.data.VersionedParameter

Get the parameter version.

getVersion() - Method in interface net.sf.basedb.core.Identifiable

Get the version number of the item.

getVersion() - Method in interface net.sf.basedb.core.plugin.About

The version of the plugin software.

getVersion() - Method in class net.sf.basedb.core.plugin.AboutImpl

getVersion() - Static method in class net.sf.basedb.core.Version

getVersion() - Method in class net.sf.basedb.util.extensions.AboutBean

getVersion() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout

getVersionParameter(String) - Static method in class net.sf.basedb.clients.web.taglib.Head

Get query parameter to the given absolute path (including root directory).

getVersionString() - Static method in class net.sf.basedb.core.Application

Get the BASE version string.

getVersionString() - Method in class net.sf.basedb.core.data.HardwareData

getVersionString() - Method in class net.sf.basedb.core.data.PluginDefinitionData

Get the version of the plugin.

getVersionString() - Method in class net.sf.basedb.core.data.SoftwareData

getVersionString() - Method in class net.sf.basedb.core.Hardware

Get the versionstring of this Hardware item.

getVersionString() - Method in class net.sf.basedb.core.PluginDefinition

Get the version of the plugin.

getVersionString() - Method in class net.sf.basedb.core.Software

Get the versionstring of this Software item.

getVersionSuffix() - Method in class net.sf.basedb.core.Application

Get the version suffix (eg.

getVirtualColumn() - Method in class net.sf.basedb.core.ExtraValue

Get the virtual column object that represents the column where the extra values are stored.

getVirtualDb() - Method in class net.sf.basedb.core.BioAssaySet

Get the virtual database this bioassayset stores it's data in.

getVirtualDb() - Method in interface net.sf.basedb.core.ClonableReporterQuery

Get the virtual database that the query is using.

getVirtualDb() - Method in class net.sf.basedb.core.data.DataCubeData

Get the virtual database this cube belongs to.

getVirtualDb() - Method in class net.sf.basedb.core.data.ExperimentData

Get the virtual database this experiment stores the analyzed data in.

getVirtualDb() - Method in class net.sf.basedb.core.DataCube

Get the virtual database this cube is a part of.

getVirtualDb() - Method in class net.sf.basedb.core.DataCubeColumn

Get the virtual database this column belongs to.

getVirtualDb() - Method in class net.sf.basedb.core.DataCubeExtraValue

Get the virtual database this extra value belongs to.

getVirtualDb() - Method in class net.sf.basedb.core.DataCubeFilter

Get the virtual database this filter belongs to.

getVirtualDb() - Method in class net.sf.basedb.core.DataCubeLayer

Get the virtual database this layer belongs to.

getVirtualDb() - Method in class net.sf.basedb.core.DynamicQuery

Get the virtual database that this query is using.

getVirtualDb() - Method in class net.sf.basedb.core.DynamicReporterQuery

Get the virtual database that this query is using.

getVirtualDb() - Method in class net.sf.basedb.core.Experiment

Get the virtual database ite that is used to manage experiment-specific tables in the dynamic database for this experiment.

getVirtualDb() - Method in class net.sf.basedb.core.ExtraValue

getVirtualTable() - Method in class net.sf.basedb.core.DataCubeExtraValue

Get the virtual table this extra value stores it's data in.

getVirtualTable() - Method in class net.sf.basedb.core.ExtraValue

getVirtualTable(Type) - Method in enum class net.sf.basedb.core.ExtraValue.CoordinateType

Get the VirtualTable used to store extra values of this coordinate type given the value type.

getVisibleColumns() - Method in class net.sf.basedb.clients.web.taglib.table.Table

getWaitingJobs() - Method in class net.sf.basedb.core.JobAgent

Get a query that returns all jobs that are waiting to be executed sorted by their priority taking the priority boost into account.

getWebAppClassLoader() - Method in class net.sf.basedb.clients.web.extensions.XJspCompiler

Get the class loader for the web application this JSP is located in.

getWell() - Method in class net.sf.basedb.core.data.FeatureData

Get the well of the feature.

getWell(int, int) - Method in class net.sf.basedb.core.Plate

Get the well on the specified plate coordinate.

getWell(DbControl, FeatureData) - Static method in class net.sf.basedb.core.Feature

Get the well from a feature.

getWells() - Method in class net.sf.basedb.core.data.PlateData

The wells on this plate.

getWells() - Method in class net.sf.basedb.core.Plate

Get a query returning all wells for this plate.

getWhichItemsParameter() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport

getWhichPropertiesParameter() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport

getWidth() - Method in interface net.sf.basedb.clients.web.extensions.plot.PlotGenerator

Get the width of the generated image.

getWidth() - Method in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean

getWidth() - Method in class net.sf.basedb.core.AnnotationType

Get the recommended width in characters a client application should use to render an input field for annotations of this annotation type.

getWidth() - Method in class net.sf.basedb.core.data.AnnotationTypeData

The recommended width (characters) to display input fields for this annotation in client applications.

getWidth() - Method in class net.sf.basedb.core.ParameterType

Get the width of the input field in the GUI.

getWorkbook() - Method in class net.sf.basedb.util.excel.XlsxTableWriter

Get the workbook.

getWorkbook() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil

Get the current workbook.

getWorkbookAsCsv() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil

Convert all sheets in the workbook to a single CSV-like stream.

getWorkingDirectory() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

Get the current working directory were data files for the external program are stored.

getWriteableFile() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile

Get a writeable view for the current file.

getWriteTrailingColumns() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil

If TRUE, trailing empty columns are written to the CSV file so that all lines have the same number of columns.

getX() - Method in class net.sf.basedb.core.data.RawData

getX() - Method in class net.sf.basedb.util.plot.HistogramPlot.TempSeries

getX(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset

getXml(String, URL, boolean) - Static method in class net.sf.basedb.util.XmlUtil2

Parse a string containing XML, optionally validating it against a DTD, and return it as a Document object.

getXmlLoader() - Method in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor

Get the loader the processor is using for parsing xml files with plug-in definitions.

getXmlLoader() - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor

Get the loader the processor is using for parsing xml files with extension definitions.

getXmlStream() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile

Get an input stream for reading the XML file containing the extension definitions.

getXValue(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset

getY() - Method in class net.sf.basedb.core.data.RawData

getY() - Method in class net.sf.basedb.util.plot.HistogramPlot.TempSeries

getY(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset

getYValue(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset

getZipFile(DbControl) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker

Get the file that is going to be unpacked by the plugin.

getZipFileParameter(String, String) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker

Get a plugin parameter that asks for the file that is going to be unpacked.

GlobalDefaultSetting - Class in net.sf.basedb.core

This class is used to represent a global default setting.

GlobalDefaultSetting(GlobalDefaultSettingData) - Constructor for class net.sf.basedb.core.GlobalDefaultSetting

GLOBALDEFAULTSETTING - Enum constant in enum class net.sf.basedb.core.Item

The item is an GlobalDefaultSetting.

GlobalDefaultSettingData - Class in net.sf.basedb.core.data

GlobalDefaultSettingData() - Constructor for class net.sf.basedb.core.data.GlobalDefaultSettingData

globalSignalId - Variable in class net.sf.basedb.core.signal.AbstractSignalTransporter

globalVersion - Static variable in class net.sf.basedb.clients.web.taglib.Head

grant(Set<Permission>) - Static method in enum class net.sf.basedb.core.Permission

Combine the given permission and convert to the integer grant value.

grant(Permission) - Static method in enum class net.sf.basedb.core.Permission

Convert the given permission to the integer grant value.

grant(Permission...) - Static method in enum class net.sf.basedb.core.Permission

Combine the given permissions and convert to the integer grant value.

granted - Variable in class net.sf.basedb.core.data.keyring.PluginKeys

granted - Variable in class net.sf.basedb.core.data.PluginPermission

granted - Variable in class net.sf.basedb.core.PluginPermission

grantValue - Variable in enum class net.sf.basedb.core.Permission

grantValue() - Method in enum class net.sf.basedb.core.Permission

GreaterConverter - Class in net.sf.basedb.util.jep.convert

Convert the '>' operator to a Query API Restriction.

GreaterConverter() - Constructor for class net.sf.basedb.util.jep.convert.GreaterConverter

GreaterEqualsConverter - Class in net.sf.basedb.util.jep.convert

Convert the '>=' operator to a Query API Restriction.

GreaterEqualsConverter() - Constructor for class net.sf.basedb.util.jep.convert.GreaterEqualsConverter

group - Variable in class net.sf.basedb.core.data.DiskUsageData

group(Expression) - Method in class net.sf.basedb.core.AbstractEntityQuery

Not supported.

group(Expression) - Method in class net.sf.basedb.core.AbstractQuery

group(Expression) - Method in interface net.sf.basedb.core.query.Query

Add an expression query element to the group list.

Group - Class in net.sf.basedb.core

This class is used to represent groups.

Group(GroupData) - Constructor for class net.sf.basedb.core.Group

GROUP - Enum constant in enum class net.sf.basedb.core.Item

The item is a Group.

Group.QueryRuntimeFilterImpl - Class in net.sf.basedb.core

A runtime filter implementation that limits a query to only return groups where the logged in user is a member unless the logged in user has generic read permission.

GROUPBY - Enum constant in enum class net.sf.basedb.core.query.QuerySection

GroupData - Class in net.sf.basedb.core.data

This class holds information about a group.

GroupData() - Constructor for class net.sf.basedb.core.data.GroupData

GroupGroups - Class in net.sf.basedb.core.data.keyring

Class for mapping the GroupGroups table.

GroupGroups() - Constructor for class net.sf.basedb.core.data.keyring.GroupGroups

Create a new GroupGroups object.

groupId - Variable in class net.sf.basedb.core.data.keyring.GroupKeys

groupId - Variable in class net.sf.basedb.core.data.keyring.GroupProjects

groupId - Variable in class net.sf.basedb.core.data.keyring.UserGroups

GroupKeys - Class in net.sf.basedb.core.data.keyring

Class for mapping the GroupKeys table.

GroupKeys() - Constructor for class net.sf.basedb.core.data.keyring.GroupKeys

Create a new GroupKeys object.

groupPermanent(Expression) - Method in class net.sf.basedb.core.AbstractEntityQuery

Not supported.

groupPermanent(Expression) - Method in class net.sf.basedb.core.AbstractQuery

groupPermanent(Expression) - Method in interface net.sf.basedb.core.query.Query

Permanently add an expression query element to the group list.

groupPermissions - Variable in class net.sf.basedb.core.GroupPermissions

groupPermissions - Variable in class net.sf.basedb.core.MultiPermissions

GroupPermissions - Class in net.sf.basedb.core

This class is used to specify permissions to share an item to groups.

GroupPermissions() - Constructor for class net.sf.basedb.core.GroupPermissions

Create a new empty object.

GroupPermissions(ItemKey) - Constructor for class net.sf.basedb.core.GroupPermissions

Create a new object, and initialise it with the permissions from a ItemKey.

GroupProjects - Class in net.sf.basedb.core.data.keyring

Class for mapping the GroupProjects table.

GroupProjects() - Constructor for class net.sf.basedb.core.data.keyring.GroupProjects

Create a new GroupProjects object.

groups - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary

groups - Variable in class net.sf.basedb.core.AbstractQuery

List of group expressions added to the query.

groups - Variable in class net.sf.basedb.core.data.ItemKeyData

groups - Variable in class net.sf.basedb.core.data.ProjectData

groups - Variable in class net.sf.basedb.core.data.UserData

groups - Variable in class net.sf.basedb.core.Keyring

Holds the ID of all groups that the user is a member of, directly or indirectly.

groups - Variable in class net.sf.basedb.core.query.SharedToRestriction

groupsWithNonHiddenMembers - Variable in class net.sf.basedb.core.Keyring

A subset of the 'groups' set that holds the id of the groups that has hiddenMembers = false

gt(Expression, Expression) - Static method in class net.sf.basedb.core.query.Restrictions

Compare if one expression is greater than another: new restriction = e1 > e2.

GT - Enum constant in enum class net.sf.basedb.core.Operator

GT - Static variable in class net.sf.basedb.clients.web.util.HTML

gteq(Expression, Expression) - Static method in class net.sf.basedb.core.query.Restrictions

Compare if one expression is greater than or equal to another: new restriction = e1 >= e2.

GTEQ - Enum constant in enum class net.sf.basedb.core.Operator

GteqRestriction - Class in net.sf.basedb.core.query

Compare if one expression is greater than or equal to another: e1 > e2.

GteqRestriction(Expression, Expression) - Constructor for class net.sf.basedb.core.query.GteqRestriction

GtfInputStream - Class in net.sf.basedb.util.gtf

Input stream implementation that reads from a GTF file and converts it to a simple tab-separated file with a single line of column headers.

GtfInputStream(InputStream, String, boolean) - Constructor for class net.sf.basedb.util.gtf.GtfInputStream

Create a new input stream reading from the master.

GtfInputStream.Attribute - Class in net.sf.basedb.util.gtf

GtfReporterImporter - Class in net.sf.basedb.plugins.gtf

Reporter importer implementation that create reporters from information in GTF files.

GtfReporterImporter() - Constructor for class net.sf.basedb.plugins.gtf.GtfReporterImporter

GtfReporterMapImporter - Class in net.sf.basedb.plugins.gtf

Import features to an array design from a GTF file.

GtfReporterMapImporter() - Constructor for class net.sf.basedb.plugins.gtf.GtfReporterMapImporter

GtfValidationAction - Class in net.sf.basedb.util.gtf

Action for validation of GTF files in a file set.

GtfValidationAction(DbControl, ArrayDesign, int) - Constructor for class net.sf.basedb.util.gtf.GtfValidationAction

Create a new action.

GtfValidationFactory - Class in net.sf.basedb.util.gtf

Action factory for creating GTF file validators.

GtfValidationFactory() - Constructor for class net.sf.basedb.util.gtf.GtfValidationFactory

GtRestriction - Class in net.sf.basedb.core.query

Compare if one expression is greater than another: e1 > e2.

GtRestriction(Expression, Expression) - Constructor for class net.sf.basedb.core.query.GtRestriction

GUEST - Static variable in class net.sf.basedb.core.Role

The id for the Role item representing guests.

guiContext - Variable in class net.sf.basedb.clients.web.extensions.JspContext

GuiContext - Class in net.sf.basedb.core.plugin

GuiContext(Item, GuiContext.Type) - Constructor for class net.sf.basedb.core.plugin.GuiContext

GuiContext(Item, GuiContext.Type, String) - Constructor for class net.sf.basedb.core.plugin.GuiContext

GuiContext.Type - Enum Class in net.sf.basedb.core.plugin

GuiContextData - Class in net.sf.basedb.core.data

This is a helper component for the PluginDefinitionData item to store the contexts where a plugin can be used in a client application.

GuiContextData() - Constructor for class net.sf.basedb.core.data.GuiContextData

GuiContextData(int, int) - Constructor for class net.sf.basedb.core.data.GuiContextData

guiContexts - Static variable in class net.sf.basedb.clients.web.plugins.SimpleExport

guiContexts - Variable in class net.sf.basedb.core.data.PluginDefinitionData

guiContexts - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

guiContexts - Static variable in class net.sf.basedb.plugins.BaseFileExporterPlugin

guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter

guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter

guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.ArraySlideImporter

guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter

guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.BioSourceImporter

guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.ExtractImporter

guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.FileImporter

guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.KitImporter

guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter

guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.SampleImporter

guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.TagImporter

guiContexts - Static variable in class net.sf.basedb.plugins.BfsExporterPlugin

guiContexts - Static variable in class net.sf.basedb.plugins.CdfFileReporterImporter

guiContexts - Static variable in class net.sf.basedb.plugins.FormulaFilter

guiContexts - Static variable in class net.sf.basedb.plugins.GalExporter

guiContexts - Static variable in class net.sf.basedb.plugins.HelpExporter

guiContexts - Static variable in class net.sf.basedb.plugins.HelpImporter

guiContexts - Static variable in class net.sf.basedb.plugins.IlluminaRawDataImporter

guiContexts - Static variable in class net.sf.basedb.plugins.IntensityCalculatorPlugin

guiContexts - Static variable in class net.sf.basedb.plugins.JepExtraValueCalculator

guiContexts - Static variable in class net.sf.basedb.plugins.JepIntensityTransformer

guiContexts - Static variable in class net.sf.basedb.plugins.PackedFileExporter

guiContexts - Static variable in class net.sf.basedb.plugins.PlateFlatFileImporter

guiContexts - Static variable in class net.sf.basedb.plugins.PlateMappingExporter

guiContexts - Static variable in class net.sf.basedb.plugins.PlateMappingImporter

guiContexts - Static variable in class net.sf.basedb.plugins.PluginConfigurationExporter

guiContexts - Static variable in class net.sf.basedb.plugins.PluginConfigurationImporter

guiContexts - Static variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter

guiContexts - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

guiContexts - Static variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

guiContexts - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

guiContexts - Static variable in class net.sf.basedb.util.zip.AbstractFileUnpacker

The context is always [ FILE, ITEM].

guiTitle - Variable in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField

guiTitle - Variable in class net.sf.basedb.plugins.BfsExporterPlugin.ExtendedExportableField

gzip - Variable in class net.sf.basedb.util.zip.GzipFilePacker

GzipFilePacker - Class in net.sf.basedb.util.zip

This class wraps the TarFilePacker in a GZIP stream, creating a tar.gz file.

GzipFilePacker() - Constructor for class net.sf.basedb.util.zip.GzipFilePacker

Create a new packer that compresses files with the gzip format.

GzipFileUnpacker - Class in net.sf.basedb.plugins

A plugin for unpacking a gzipped file to the BASE file system.

GzipFileUnpacker() - Constructor for class net.sf.basedb.plugins.GzipFileUnpacker

H

H_BOOLEAN - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper

H_DATE - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper

H_DOUBLE - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper

H_FLOAT - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper

H_INTEGER - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper

H_LONG - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper

H_SHORT - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper

H_STRING - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper

H_TEXT - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper

H_TIMESTAMP - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper

handleBof(EventHandler, String) - Method in class net.sf.basedb.util.bfs.MetadataParser

Handle the beginning-of-file marker event.

handleCmd(Socket, String) - Method in class net.sf.basedb.clients.jobagent.handlers.DefaultRequestHandler

handleCmd(Socket, String) - Method in class net.sf.basedb.clients.jobagent.handlers.InfoRequestHandler

handleCmd(Socket, String) - Method in class net.sf.basedb.clients.jobagent.handlers.MultiProtocolRequestHandler

handleCmd(Socket, String) - Method in class net.sf.basedb.clients.jobagent.handlers.PauseRequestHandler

handleCmd(Socket, String) - Method in class net.sf.basedb.clients.jobagent.handlers.PingRequestHandler

handleCmd(Socket, String) - Method in class net.sf.basedb.clients.jobagent.handlers.SignalRequestHandler

handleCmd(Socket, String) - Method in class net.sf.basedb.clients.jobagent.handlers.StartRequestHandler

handleCmd(Socket, String) - Method in class net.sf.basedb.clients.jobagent.handlers.StopRequestHandler

handleCmd(Socket, String) - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlotRequestHandler

handleCmd(Socket, String) - Method in interface net.sf.basedb.util.jobagent.RequestHandler

Handle a command that was sent by an incoming request.

handleData(EventHandler, String[]) - Method in class net.sf.basedb.util.bfs.AnnotationParser

Handle the data event.

handleData(EventHandler, String[]) - Method in class net.sf.basedb.util.bfs.DataParser

Handle the data event.

handleData(FlatFileParser.Data) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

Called by the parser for every line in the file that is a data line.

handleData(FlatFileParser.Data) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter

Read annotations from a single data line.

handleData(FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

handleData(FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

handleData(FlatFileParser.Data) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter

handleData(FlatFileParser.Data) - Method in class net.sf.basedb.plugins.PlateFlatFileImporter

handleData(FlatFileParser.Data) - Method in class net.sf.basedb.plugins.PlateMappingImporter

Add a mapping detail.

handleData(FlatFileParser.Data) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter

handleData(FlatFileParser.Data) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter

handleData(FlatFileParser.Data) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter

handleData(FlatFileParser.Data) - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

handleEndOfFile(EventHandler) - Method in class net.sf.basedb.util.bfs.AnnotationParser

Handle the end-of-file event.

handleEndOfFile(EventHandler) - Method in class net.sf.basedb.util.bfs.DataParser

Handle the end-of-file event.

handleEndOfFile(EventHandler) - Method in class net.sf.basedb.util.bfs.MetadataParser

Handle the end-of-file event.

handleEntry(EventHandler, MetadataModel.SectionEntry) - Method in class net.sf.basedb.util.bfs.MetadataParser

Handle the section entry event.

handleError(A, String, Throwable) - Method in class net.sf.basedb.util.extensions.ExtensionContext

handleError(String, Throwable) - Method in class net.sf.basedb.util.extensions.ExtensionContext

handleError(String, Throwable) - Method in class net.sf.basedb.util.extensions.ExtensionPointContext

handleError(Throwable) - Method in class net.sf.basedb.util.error.ClassMapErrorHandler

handleError(Throwable) - Method in interface net.sf.basedb.util.error.ErrorHandler

Handle an error.

handleError(Throwable) - Method in class net.sf.basedb.util.error.SimpleErrorHandler

Return TRUE if all errors should be ignored, otherwise re-throw the throwable.

handleError(InvokationContext<? extends A>, A, String, Throwable) - Method in interface net.sf.basedb.util.extensions.ErrorHandler

Handle an exception that has happened.

handleError(InvokationContext<? extends Action>, Action, String, Throwable) - Method in class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory

handleError(InvokationContext<? extends Action>, Action, String, Throwable) - Method in class net.sf.basedb.util.extensions.RethrowErrorHandlerFactory

handleEvent(EventType<T>, T, BfsParser) - Method in class net.sf.basedb.util.bfs.AnnotationModel

handleEvent(EventType<T>, T, BfsParser) - Method in interface net.sf.basedb.util.bfs.EventHandler

The method is called by the parser when it has found something interesting in a BFS file.

handleEvent(EventType<T>, T, BfsParser) - Method in class net.sf.basedb.util.bfs.MatrixModel

handleEvent(EventType<T>, T, BfsParser) - Method in class net.sf.basedb.util.bfs.MultiEventHandler

Resends the incoming event to all registered event handlers.

handleEvent(EventType, Object, BfsParser) - Method in class net.sf.basedb.util.bfs.MetadataModel

handleEvent(EventType, Object, BfsParser) - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter.ProgressEventHandler

handleEvent(EventType, Object, BfsParser) - Method in class net.sf.basedb.util.importer.spotdata.MatrixSpotIntensityEventHandler

Extract the spot intensity values from the data files and batch insert them using the spot batcher.

handleEvent(EventType, Object, BfsParser) - Method in class net.sf.basedb.util.importer.spotdata.PositionEventHandler

Get the position number from the given parser/column.

handleEvent(EventType, Object, BfsParser) - Method in class net.sf.basedb.util.importer.spotdata.SerialSpotIntensityEventHandler

Extract the spot intensity values from the data files and batch insert them using the spot batcher.

handleEvent(EventType) - Method in class net.sf.basedb.util.extensions.ActionIterator

Send the event to event handlers registered in the registry.

handleEvent(EventType, ExtensionPoint<?>, Extension<?>) - Method in class net.sf.basedb.clients.web.extensions.service.ServicesEventHandler

handleEvent(EventType, ExtensionPoint<?>, Extension<?>) - Method in interface net.sf.basedb.util.extensions.events.EventHandler

Handle an event.

handleEvent(EventType, ExtensionPoint<?>, Extension<?>) - Method in class net.sf.basedb.util.extensions.Registry

Send an event to all event handlers.

handleHeader(EventHandler, String[]) - Method in class net.sf.basedb.util.bfs.AnnotationParser

Handle the header-found event.

handleHeader(FlatFileParser.Line) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

Called by the parser for every line in the file that is a header line.

handleHeader(FlatFileParser.Line) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter

Copy headers so that we can set them on the raw bioassays in beginData()

handleHeader(FlatFileParser.Line) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter

handleHeader(FlatFileParser.Line) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter

handleInterrupt() - Method in class net.sf.basedb.core.signal.EnhancedThreadSignalHandler

Throws a SignalReceivedException if one ore more signals has been received.

handleInterrupt() - Method in class net.sf.basedb.core.signal.ExceptionInterruptHandler

handleInterrupt() - Method in interface net.sf.basedb.core.signal.InterruptHandler

This method is called when the worker thread has been interrupted by some other thread.

handler - Variable in class net.sf.basedb.clients.web.util.SimpleSignalProgressReporter

handler - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredEventHandler

handlerIds - Variable in class net.sf.basedb.core.signal.AbstractSignalReceiver

handlers - Variable in class net.sf.basedb.clients.jobagent.handlers.MultiProtocolRequestHandler

handlers - Variable in class net.sf.basedb.core.signal.AbstractSignalReceiver

Maps local signal handler ID to -> signal handler itself.

handlers - Variable in class net.sf.basedb.core.signal.DelegatingSignalHandler

Holds the registered signal handlers.

handlers - Variable in class net.sf.basedb.util.bfs.MultiEventHandler

handleSection(EventHandler, String) - Method in class net.sf.basedb.util.bfs.MetadataParser

Handle the new section event.

handleSection(FlatFileParser.Line) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

Called by the parser for every line in the file that is a section line.

handleSection(FlatFileParser.Line) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter

handleSectionEnd(EventHandler, String) - Method in class net.sf.basedb.util.bfs.MetadataParser

Handle the end-of-section event.

handleSignal(Signal) - Method in class net.sf.basedb.core.signal.DelegatingSignalHandler

Handler the given signal by invoking SignalHandler.handleSignal(Signal) on each registered signal handler.

handleSignal(Signal) - Method in class net.sf.basedb.core.signal.EnhancedThreadSignalHandler

When a supported signal is received Thread.interrupt() is called on the worker thread that was registered when this object was created.

handleSignal(Signal) - Method in class net.sf.basedb.core.signal.ForwardingSignalHandler

Forwards the signal to the signal transporter given in the constructor.

handleSignal(Signal) - Method in class net.sf.basedb.core.signal.ProgressReporterSignalHandler

When signals are receieved, they are stored in a temporary list in the order they come in.

handleSignal(Signal) - Method in interface net.sf.basedb.core.signal.SignalHandler

Handle the given signal.

handleSignal(Signal) - Method in class net.sf.basedb.core.signal.ThreadSignalHandler

Only handles the Signal.ABORT signal.

hardware - Variable in class net.sf.basedb.core.data.BioMaterialEventData

hardware - Variable in class net.sf.basedb.core.data.BioPlateEventData

hardware - Variable in class net.sf.basedb.core.data.DerivedBioAssayData

hardware - Variable in class net.sf.basedb.core.data.PlateEventData

Hardware - Class in net.sf.basedb.core

This class is used to represent individual hardware items and information about them.

Hardware(HardwareData) - Constructor for class net.sf.basedb.core.Hardware

Creates a new hardware item.

HARDWARE - Enum constant in enum class net.sf.basedb.core.Item

The item is a Hardware.

hardwareColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter

hardwareColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter

hardwareColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

hardwareColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter

HardwareData - Class in net.sf.basedb.core.data

This class holds information about a Hardware.

HardwareData() - Constructor for class net.sf.basedb.core.data.HardwareData

hardwareHasBeenSet - Variable in class net.sf.basedb.core.BioMaterialEvent

hardwareHasBeenSet - Variable in class net.sf.basedb.core.DerivedBioAssay

HardwareLoader - Class in net.sf.basedb.util.overview.loader

Node loader implementation for hardware.

HardwareLoader() - Constructor for class net.sf.basedb.util.overview.loader.HardwareLoader

hardwareMapper - Variable in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter

hardwareMapper - Variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter

hardwareMapper - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

hardwareMapper - Variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter

hardwareQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

HardwareValidator - Class in net.sf.basedb.util.overview.validator

Validator implementation for hardware.

HardwareValidator() - Constructor for class net.sf.basedb.util.overview.validator.HardwareValidator

HAS_CANCELBUTTON - Static variable in class net.sf.basedb.clients.web.ModeInfo

HAS_CHECK - Static variable in class net.sf.basedb.clients.web.ModeInfo

HAS_CLOSEBUTTON - Static variable in class net.sf.basedb.clients.web.ModeInfo

HAS_EDITLINK - Static variable in class net.sf.basedb.clients.web.ModeInfo

HAS_FILTER - Static variable in class net.sf.basedb.clients.web.ModeInfo

HAS_ICONS - Static variable in class net.sf.basedb.clients.web.ModeInfo

HAS_NAVIGATOR - Static variable in class net.sf.basedb.clients.web.ModeInfo

HAS_OKBUTTON - Static variable in class net.sf.basedb.clients.web.ModeInfo

HAS_PROPERTYLINK - Static variable in class net.sf.basedb.clients.web.ModeInfo

HAS_RADIO - Static variable in class net.sf.basedb.clients.web.ModeInfo

HAS_TOOLBAR - Static variable in class net.sf.basedb.clients.web.ModeInfo

hasAborted - Variable in class net.sf.basedb.core.signal.ThreadSignalHandler

If TRUE, at least one ABORT signal has been recieved.

hasAborted() - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress

Check if the upload has been requested to be aborted.

hasActiveValidator(DbControl) - Method in class net.sf.basedb.core.DataFileType

Check if there is at least one extension that claims to support validation of files of this type.

hasAllRequiredFiles() - Method in class net.sf.basedb.core.FileSet

Checks if this file set contains a file for each DataFileType that is required according to what has been specified by the Platform and PlatformVariant.

hasAnnotatableItem - Variable in class net.sf.basedb.core.MultiPermissions

hasAnnotatableItem() - Method in class net.sf.basedb.core.MultiPermissions

Is any of the items to share an annotatable item?

hasAnnotation(AnnotationType, Annotation.Source) - Method in class net.sf.basedb.core.AnnotationSet

Check if the annotation set contains an annotation of the specified type.

HasAnnotationRestriction - Class in net.sf.basedb.core

Restricts a query by the presence of absence of an annotation.

HasAnnotationRestriction(String, int, boolean, boolean, boolean) - Constructor for class net.sf.basedb.core.HasAnnotationRestriction

Deprecated.

In 3.11, use HasAnnotationRestriction(String, AnnotationType, boolean, AnnotationRestriction.Options) instead

HasAnnotationRestriction(String, AnnotationType, boolean, boolean, boolean) - Constructor for class net.sf.basedb.core.HasAnnotationRestriction

Deprecated.

In 3.11, use HasAnnotationRestriction(String, AnnotationType, boolean, AnnotationRestriction.Options) instead

HasAnnotationRestriction(String, AnnotationType, boolean, AnnotationRestriction.Options) - Constructor for class net.sf.basedb.core.HasAnnotationRestriction

Create a new restriction that checks if an item has been annotatated or not.

hasArrayDesign() - Method in class net.sf.basedb.core.RawBioAssay

Check if this raw bioassay is connected to an array design or not.

hasAttribute(NodeAttribute<?>) - Method in class net.sf.basedb.util.overview.Node

Check if the node has a value for the given attribute.

HasAttributeFilter - Class in net.sf.basedb.util.overview.filter

A filter implementation that checks if a value for a given attribute exists on a node.

HasAttributeFilter(NodeAttribute<?>) - Constructor for class net.sf.basedb.util.overview.filter.HasAttributeFilter

Create a filter that finds nodes that has value for the given attribute.

HasAttributeFilter(NodeAttribute<?>, Object) - Constructor for class net.sf.basedb.util.overview.filter.HasAttributeFilter

Create a filter that finds nodes that has a specific value for the given attribute.

hasAutoJoined - Variable in class net.sf.basedb.core.AbstractQuery

hasBeenAccepted - Variable in class net.sf.basedb.util.fileset.ValidatingFileSetMember

hasBeenAccepted() - Method in class net.sf.basedb.util.fileset.ValidatingFileSetMember

Has this member been accepted for validation by at least one validator?

hasBeenAnnotatated - Variable in class net.sf.basedb.core.HasAnnotationRestriction

hasBeenCalledFromAnnotationBatcher - Variable in class net.sf.basedb.core.BasicItem

hasBeenCalledFromGetAnnotationSet - Variable in class net.sf.basedb.core.BasicItem

hasBeenUsed - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo

hasBeenUsed() - Method in class net.sf.basedb.core.BioWell

If the original biomaterial in this well has been moved to another plate (eg. for final storage in a freezer).

hasBom - Variable in class net.sf.basedb.util.basefile.BaseFileWriter

hasCancelButton - Variable in class net.sf.basedb.clients.web.ModeInfo

hasCancelButton() - Method in class net.sf.basedb.clients.web.ModeInfo

hasCategoryOrSubtype(AnnotationTypeCategory, ItemSubtype) - Method in class net.sf.basedb.core.ItemContext

Checks if this context has a matching category or subtype.

hasChanged - Variable in class net.sf.basedb.util.extensions.manager.Settings

hasChanged() - Method in class net.sf.basedb.util.JarClassLoader.JarClassLoaderProxy

hasChanged(boolean) - Method in class net.sf.basedb.util.JarClassLoader

Check if the JAR file this class loader loads is classes from has changed since this class loader was created.

hasChanged(Group) - Method in class net.sf.basedb.core.GroupPermissions

Check if the current permissions for the group has been changed from the original permissions.

hasChanged(Project) - Method in class net.sf.basedb.core.ProjectPermissions

Check if the current permissions for the project has been changed from the original permissions.

hasChanged(User) - Method in class net.sf.basedb.core.UserPermissions

Check if the current permissions for the user has been changed from the original permissions.

hasCheck - Variable in class net.sf.basedb.clients.web.ModeInfo

hasCheck() - Method in class net.sf.basedb.clients.web.ModeInfo

hasClonableProperty(String) - Method in class net.sf.basedb.core.ReporterCloneTemplate

Check if this template contains a clonable property with the given name.

hasClonedReporterProperty(String) - Method in class net.sf.basedb.core.VirtualDb

Checks if this virtual db has cloned the given reporter property or not.

hasClonedReporters - Variable in class net.sf.basedb.core.DynamicQuery

hasClonedReporters - Variable in class net.sf.basedb.core.DynamicReporterQuery

hasClonedReporters() - Method in interface net.sf.basedb.core.ClonableReporterQuery

Check if the virtual database that this query is using has cloned reporter annotations or not.

hasClonedReporters() - Method in class net.sf.basedb.core.DynamicQuery

Check if the virtual database that this query is using has cloned reporter annotations or not.

hasClonedReporters() - Method in class net.sf.basedb.core.DynamicReporterQuery

Check if the virtual database that this query is using has cloned reporter annotations or not.

hasClonedReporters() - Method in class net.sf.basedb.core.VirtualDb

Check if this virtual db is storing cloned reporter information or not.

hasCloseButton - Variable in class net.sf.basedb.clients.web.ModeInfo

hasCloseButton() - Method in class net.sf.basedb.clients.web.ModeInfo

hasColumn(VirtualColumn) - Method in enum class net.sf.basedb.core.VirtualTable

Check if the specified column is part of the virtual table or not.

hasCompleted - Variable in class net.sf.basedb.util.uri.http.HttpConnectionManager.TimeoutTimer

hasContext() - Method in class net.sf.basedb.core.Job

Checks if this job has saved information about the context that was active when this job was created.

hasCreatedRenderer - Variable in class net.sf.basedb.util.extensions.ExtensionContext

hasCreatedRenderer - Variable in class net.sf.basedb.util.extensions.ExtensionPointContext

hasData - Variable in class net.sf.basedb.core.data.RawBioAssayData

hasData() - Method in class net.sf.basedb.core.RawBioAssay

If raw data has been added to this raw bioassay or not.

hasDataFile(DbControl, FileStoreEnabled, String, boolean) - Static method in class net.sf.basedb.core.FileStoreUtil

Check if a file of the given data file type is present in a FileStoreEnabled item's file set.

hasDataNo - Variable in class net.sf.basedb.util.parser.JepMapper

hasDatePart(String) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil

hasDefaultForItem(BasicItem) - Method in class net.sf.basedb.core.Project

Check if the project has a default item that has the same class and subtype as the given item.

hasDefaultOfType(Item, ItemSubtype) - Method in class net.sf.basedb.core.Project

Check if the project has a default item of the given item type and (optional) subtype.

hasDisabledRawJoin() - Method in class net.sf.basedb.core.DynamicSpotQuery

Check if joining to raw data has been disabled.

hasEditLink - Variable in class net.sf.basedb.clients.web.ModeInfo

hasEditLink() - Method in class net.sf.basedb.clients.web.ModeInfo

hasError - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper

hasError - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile

hasError - Variable in class net.sf.basedb.util.extensions.manager.ProcessResults.FileResults

hasError - Variable in class net.sf.basedb.util.extensions.manager.ProcessResults

hasError() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper

hasError() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile

If there was an error when registering the extensions in this file.

hasError() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults.FileResults

If there was an error in this file or not.

hasError() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults

Check if the scan was successful or not.

hasError() - Method in class net.sf.basedb.util.FileCopyRunnable

A boolean flag indicating if the copying was sucessful or not.

hasEvent(PlateEventType) - Method in class net.sf.basedb.core.Plate

Check if an event for the specified event type has been created for this plate.

hasExceededQuota(QuotaType, Location) - Method in class net.sf.basedb.core.User

Check if the user has used more quota than what has been assigned.

hasExtensionFilter(String) - Method in class net.sf.basedb.core.ItemContext

Checks if there is an extension filter with a property starting with !

hasExternalId(Item) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter

Check if the current item has an 'externalId' property.

hasExternalId(Item) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

Check if the current item has an 'externalId' property.

hasExtraInformation() - Method in class net.sf.basedb.core.authentication.AuthenticatedUser

Check if extra information about the user has been provided.

hasFeatures - Variable in class net.sf.basedb.core.data.ArrayDesignData

hasFeatures() - Method in class net.sf.basedb.core.ArrayDesign

Check if this array design has information about features, either in the database or in files.

hasFeatures() - Method in class net.sf.basedb.core.ArrayDesignBlock

Checks if this ArrayDesignBlock has any features.

hasFileSet() - Method in class net.sf.basedb.core.ArrayDesign

hasFileSet() - Method in class net.sf.basedb.core.BioAssaySet

hasFileSet() - Method in class net.sf.basedb.core.DerivedBioAssay

hasFileSet() - Method in class net.sf.basedb.core.ExtraValue

hasFileSet() - Method in interface net.sf.basedb.core.FileStoreEnabled

Check if this item has a file set.

hasFileSet() - Method in class net.sf.basedb.core.RawBioAssay

hasFilter - Variable in class net.sf.basedb.clients.web.ModeInfo

hasFilter() - Method in class net.sf.basedb.clients.web.ModeInfo

HASH - Static variable in class net.sf.basedb.clients.web.util.HTML

hashCode - Variable in class net.sf.basedb.core.data.BasicData

Stores the hash code of the item.

hashCode - Variable in class net.sf.basedb.core.DynamicJoin

hashCode - Variable in class net.sf.basedb.core.query.AndRestriction

hashCode - Variable in class net.sf.basedb.core.query.CaseExpression

hashCode - Variable in class net.sf.basedb.core.query.InRestriction

hashCode - Variable in class net.sf.basedb.core.query.OrRestriction

hashCode() - Method in class net.sf.basedb.clients.web.extensions.ServletWrapperKey

hashCode() - Method in class net.sf.basedb.clients.web.ModeInfo.ModeContext

hashCode() - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey

hashCode() - Method in class net.sf.basedb.core.AnnotationBetweenRestriction

hashCode() - Method in class net.sf.basedb.core.AnnotationInRestriction

hashCode() - Method in class net.sf.basedb.core.AnnotationRestriction

hashCode() - Method in class net.sf.basedb.core.AnnotationSimpleRestriction

hashCode() - Method in class net.sf.basedb.core.BasicItem

The hash code is calculated at object construction and remains the same during the objects lifetime.

hashCode() - Method in class net.sf.basedb.core.BlockInfo

Calculate the hash code for the object.

hashCode() - Method in class net.sf.basedb.core.ClonableProperty

hashCode() - Method in class net.sf.basedb.core.ContextKey

Calculate the hash code for the object.

hashCode() - Method in class net.sf.basedb.core.data.BasicData

For new items (getId() returns 0) the hash code is the same as returned by the System.identityHashCode() method.

hashCode() - Method in class net.sf.basedb.core.data.ContextIndex

Calculate the hash code for the object.

hashCode() - Method in class net.sf.basedb.core.data.FileTypeIndex

Calculate the hash code for the object.

hashCode() - Method in class net.sf.basedb.core.data.GuiContextData

Calculate the hash code for the object.

hashCode() - Method in class net.sf.basedb.core.data.keyring.GroupGroups

Calculate the hash code for the object.

hashCode() - Method in class net.sf.basedb.core.data.keyring.GroupKeys

Calculate the hash code for the object.

hashCode() - Method in class net.sf.basedb.core.data.keyring.GroupProjects

Calculate the hash code for the object.

hashCode() - Method in class net.sf.basedb.core.data.keyring.PluginKeys

Calculate the hash code for the object.

hashCode() - Method in class net.sf.basedb.core.data.keyring.ProjectKeys

Calculate the hash code for the object.

hashCode() - Method in class net.sf.basedb.core.data.keyring.RoleKeys

Calculate the hash code for the object.

hashCode() - Method in class net.sf.basedb.core.data.keyring.UserGroups

Calculate the hash code for the object.

hashCode() - Method in class net.sf.basedb.core.data.keyring.UserKeys

Calculate the hash code for the object.

hashCode() - Method in class net.sf.basedb.core.data.keyring.UserProjects

Calculate the hash code for the object.

hashCode() - Method in class net.sf.basedb.core.data.keyring.UserRoles

Calculate the hash code for the object.

hashCode() - Method in class net.sf.basedb.core.data.MappingCoordinate

Calculate the hash code for the object.

hashCode() - Method in class net.sf.basedb.core.data.PlateCoordinate

Calculate the hash code for the object.

hashCode() - Method in class net.sf.basedb.core.data.QuotaIndex

Calculate the hash code for the object.

hashCode() - Method in class net.sf.basedb.core.data.ReporterListScoreData

hashCode() - Method in class net.sf.basedb.core.data.VersionedParameter

Calculate the hash code for the object.

hashCode() - Method in class net.sf.basedb.core.DynamicJoin

hashCode() - Method in class net.sf.basedb.core.DynamicRestriction

hashCode() - Method in class net.sf.basedb.core.ExtraValueExpression

hashCode() - Method in class net.sf.basedb.core.ExtraValueJoin

hashCode() - Method in class net.sf.basedb.core.FeatureCoordinate

Calculate the hash code for the object.

hashCode() - Method in class net.sf.basedb.core.HasAnnotationRestriction

hashCode() - Method in class net.sf.basedb.core.ItemProxy

The hash code is calculated from the Item.getValue() and the id.

hashCode() - Method in class net.sf.basedb.core.ItemResultList

hashCode() - Method in class net.sf.basedb.core.MeanRawDataPropertyExpression

hashCode() - Method in class net.sf.basedb.core.plugin.GuiContext

hashCode() - Method in class net.sf.basedb.core.query.AbsExpression

hashCode() - Method in class net.sf.basedb.core.query.AddExpression

hashCode() - Method in class net.sf.basedb.core.query.AndRestriction

hashCode() - Method in class net.sf.basedb.core.query.AnnotationJoin

hashCode() - Method in class net.sf.basedb.core.query.AnyToAnyRestriction

hashCode() - Method in class net.sf.basedb.core.query.AscOrder

hashCode() - Method in class net.sf.basedb.core.query.BetweenRestriction

hashCode() - Method in class net.sf.basedb.core.query.BooleanExpression

hashCode() - Method in class net.sf.basedb.core.query.CaseExpression

hashCode() - Method in class net.sf.basedb.core.query.ConditionalQueryElement

hashCode() - Method in class net.sf.basedb.core.query.CountExpression

hashCode() - Method in class net.sf.basedb.core.query.DescOrder

hashCode() - Method in class net.sf.basedb.core.query.DivideExpression

hashCode() - Method in class net.sf.basedb.core.query.EqRestriction

hashCode() - Method in class net.sf.basedb.core.query.ExpExpression

hashCode() - Method in class net.sf.basedb.core.query.ExpressionSelect

hashCode() - Method in class net.sf.basedb.core.query.FloatExpression

hashCode() - Method in class net.sf.basedb.core.query.GeometricMeanExpression

hashCode() - Method in class net.sf.basedb.core.query.GteqRestriction

hashCode() - Method in class net.sf.basedb.core.query.GtRestriction

hashCode() - Method in class net.sf.basedb.core.query.HqlElementsExpression

hashCode() - Method in class net.sf.basedb.core.query.HqlEntityExpression

hashCode() - Method in class net.sf.basedb.core.query.HqlEntityParameterExpression

hashCode() - Method in class net.sf.basedb.core.query.HqlExpression

hashCode() - Method in class net.sf.basedb.core.query.HqlIndexExpression

hashCode() - Method in class net.sf.basedb.core.query.HqlInnerJoin

hashCode() - Method in class net.sf.basedb.core.query.HqlLeftJoin

hashCode() - Method in class net.sf.basedb.core.query.HqlPropertyExpression

hashCode() - Method in class net.sf.basedb.core.query.HqlRightJoin

hashCode() - Method in class net.sf.basedb.core.query.HqlSizeExpression

hashCode() - Method in class net.sf.basedb.core.query.InRestriction

hashCode() - Method in class net.sf.basedb.core.query.IntegerExpression

hashCode() - Method in class net.sf.basedb.core.query.LikeRestriction

hashCode() - Method in class net.sf.basedb.core.query.LogExpression

hashCode() - Method in class net.sf.basedb.core.query.LteqRestriction

hashCode() - Method in class net.sf.basedb.core.query.LtRestriction

hashCode() - Method in class net.sf.basedb.core.query.MaxExpression

hashCode() - Method in class net.sf.basedb.core.query.MeanExpression

hashCode() - Method in class net.sf.basedb.core.query.MinExpression

hashCode() - Method in class net.sf.basedb.core.query.MultiplyExpression

hashCode() - Method in class net.sf.basedb.core.query.NegateExpression

hashCode() - Method in class net.sf.basedb.core.query.NeqRestriction

hashCode() - Method in class net.sf.basedb.core.query.NotRestriction

hashCode() - Method in class net.sf.basedb.core.query.OrRestriction

hashCode() - Method in class net.sf.basedb.core.query.ParameterExpression

hashCode() - Method in class net.sf.basedb.core.query.PowerExpression

hashCode() - Method in class net.sf.basedb.core.query.QuadraticMeanExpression

hashCode() - Method in class net.sf.basedb.core.query.QueryParameter

hashCode() - Method in class net.sf.basedb.core.query.ReporterListExpression

hashCode() - Method in class net.sf.basedb.core.query.RlikeRestriction

hashCode() - Method in class net.sf.basedb.core.query.SelectedExpression

hashCode() - Method in class net.sf.basedb.core.query.SharedToRestriction

hashCode() - Method in class net.sf.basedb.core.query.SqlColumnExpression

hashCode() - Method in class net.sf.basedb.core.query.SqrtExpression

hashCode() - Method in class net.sf.basedb.core.query.SubqueryExpression

hashCode() - Method in class net.sf.basedb.core.query.SubtractExpression

hashCode() - Method in class net.sf.basedb.core.query.SumExpression

hashCode() - Method in class net.sf.basedb.core.query.ToDateExpression

hashCode() - Method in class net.sf.basedb.core.query.VirtualColumnExpression

hashCode() - Method in class net.sf.basedb.core.query.WhenStatement

hashCode() - Method in class net.sf.basedb.core.RawBioAssayPropertyExpression

hashCode() - Method in class net.sf.basedb.core.RawDataPropertyExpression

hashCode() - Method in class net.sf.basedb.core.RawDataType

hashCode() - Method in class net.sf.basedb.core.RealJoin

hashCode() - Method in class net.sf.basedb.core.ReporterListJoin

hashCode() - Method in class net.sf.basedb.core.ReporterPropertyExpression

hashCode() - Method in class net.sf.basedb.core.SessionControl.MainContext

hashCode() - Method in class net.sf.basedb.core.signal.Signal

The hashcode for a signal is the same as the hashcode for the ID.

hashCode() - Method in class net.sf.basedb.core.VirtualColumn

hashCode() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField

hashCode() - Method in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper

hashCode() - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics

hashCode() - Method in class net.sf.basedb.util.export.spotdata.AnnotationAssayField

hashCode() - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField

hashCode() - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField

hashCode() - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField

hashCode() - Method in class net.sf.basedb.util.extensions.manager.ExtensionKey

hashCode() - Method in class net.sf.basedb.util.extensions.manager.ExtensionPointKey

hashCode() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile

hashCode() - Method in class net.sf.basedb.util.extensions.manager.FactoryParametersKey

hashCode() - Method in class net.sf.basedb.util.extensions.manager.PluginInfoKey

hashCode() - Method in class net.sf.basedb.util.extensions.Registry.AttributeKey

hashCode() - Method in class net.sf.basedb.util.gtf.GtfInputStream.Attribute

hashCode() - Method in class net.sf.basedb.util.jobagent.JobInfo

hashCode() - Method in class net.sf.basedb.util.listable.TransformCache.CacheKey

hashCode() - Method in class net.sf.basedb.util.overview.cache.DirectionalCacheKey

hashCode() - Method in class net.sf.basedb.util.overview.cache.IndexedCacheKey

hashCode() - Method in class net.sf.basedb.util.overview.Failure

hashCode() - Method in class net.sf.basedb.util.overview.validator.ExtractValidator.TagPosition

hashCode() - Method in class net.sf.basedb.util.Tree

hashCode() - Method in class net.sf.basedb.util.units.UnitCache.CacheKey

From the Object class ---------------------

hashCode(Object) - Static method in class net.sf.basedb.util.EqualsHelper

Get the hashcode for an object.

hashCode(T...) - Static method in class net.sf.basedb.util.EqualsHelper

Hashcode calculation for an array of objects that doesn't depend on the position in the array.

hasHiddenCharacters() - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo

If set, the input fields has hidden characters, otherwise they are visible.

hasHiddenMembers() - Method in class net.sf.basedb.core.Group

Does this group have hidden members?

hashpw(String, String) - Static method in class net.sf.basedb.util.bcrypt.BCrypt

Hash a password using the OpenBSD bcrypt scheme

hasIcons - Variable in class net.sf.basedb.clients.web.ModeInfo

hasIcons() - Method in class net.sf.basedb.clients.web.ModeInfo

hasImages - Variable in class net.sf.basedb.clients.web.taglib.table.Toolbar

If buttons should display images.

hasImages() - Method in class net.sf.basedb.clients.web.taglib.table.Toolbar

hasItemSubtype() - Method in class net.sf.basedb.core.ItemContext

Is this context limited to return items of a given subtype or not?

hasJoined - Variable in class net.sf.basedb.core.HqlQueryJoiners.AnnotationJoiner

hasLineNo - Variable in class net.sf.basedb.util.parser.JepMapper

hasLink - Variable in class net.sf.basedb.core.query.AnyToAnyRestriction

hasMember(DataFileType) - Method in class net.sf.basedb.core.FileSet

Check if the file set contains at least one file of the specified type.

hasMoreData() - Method in class net.sf.basedb.util.parser.FlatFileParser

Check if the input stream contains more data.

hasMoreSections() - Method in class net.sf.basedb.util.parser.FlatFileParser

Check if the input stream contains more sections.

hasNavigator - Variable in class net.sf.basedb.clients.web.ModeInfo

hasNavigator() - Method in class net.sf.basedb.clients.web.ModeInfo

hasNext - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef.NullIterator

hasNext - Variable in class net.sf.basedb.core.DynamicResultIterator

hasNext - Variable in class net.sf.basedb.util.extensions.ActionIterator

hasNext() - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator

hasNext() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef.NullIterator

hasNext() - Method in class net.sf.basedb.core.DataResultIterator

hasNext() - Method in class net.sf.basedb.core.DynamicResultIterator

hasNext() - Method in class net.sf.basedb.core.FastAnnotationLoader.FastIterator

hasNext() - Method in class net.sf.basedb.core.ItemResultIterator

hasNext() - Method in class net.sf.basedb.core.ItemResultList.ResultListIterator

hasNext() - Method in class net.sf.basedb.core.ItemResultList.ResultListListIterator

hasNext() - Method in class net.sf.basedb.core.ReporterScoreResultIterator

hasNext() - Method in class net.sf.basedb.core.ScrollIterator

hasNext() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter.FileIterator

hasNext() - Method in class net.sf.basedb.util.ArrayIterator

hasNext() - Method in class net.sf.basedb.util.extensions.ActionIterator

hasNext() - Method in class net.sf.basedb.util.NestedIterator

hasNext() - Method in class net.sf.basedb.util.query.MultiQueryIterator

hasNext() - Method in class net.sf.basedb.util.Tree.ElementIterator

hasNext() - Method in class net.sf.basedb.util.Tree.EntryIterator

hasOkButton - Variable in class net.sf.basedb.clients.web.ModeInfo

hasOkButton() - Method in class net.sf.basedb.clients.web.ModeInfo

hasOption(String) - Method in class net.sf.basedb.clients.jobagent.CmdLine

Check if an option was specified or not.

hasParameterValue(String) - Method in class net.sf.basedb.core.AbstractQuery

hasParameterValue(String) - Method in interface net.sf.basedb.core.query.Query

Check if a value for the specified parameter has been set or not.

hasPassword() - Method in class net.sf.basedb.core.FileServer

Is a password set or not?

hasPermission(int, Permission) - Static method in enum class net.sf.basedb.core.Permission

Checks if the given Permission is granted by the permissions code.

hasPermission(DbControl, Permission) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

Check if the logged in user has the request permission on this annotation or annotation set.

hasPermission(Permission) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

hasPermission(Permission) - Method in interface net.sf.basedb.core.AccessControlled

Check if the logged in user has the desired permission on the item.

hasPermission(Permission) - Method in class net.sf.basedb.core.BasicBatcher

Checks if the logged in user has the specified permission on this item.

hasPermission(Permission) - Method in class net.sf.basedb.core.BasicItem

Checks if the logged in user has the specified permission on this item.

hasPermission(Permission) - Method in class net.sf.basedb.core.BioMaterialEventSource

hasPermission(Permission) - Method in class net.sf.basedb.core.Coloring

hasPermission(Permission, Item) - Method in class net.sf.basedb.core.SessionControl

Check if the logged in user has the specfied permission for all item of the specified type.

hasPermission(SessionControl, Permission) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

hasPermission(ClientContext, Item, Permission) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

hasPrevious() - Method in class net.sf.basedb.core.ItemResultList.ResultListListIterator

hasPrintedHeaders - Variable in class net.sf.basedb.util.bfs.AnnotationWriter

hasPrintedHeaders() - Method in class net.sf.basedb.util.bfs.AnnotationWriter

Checks if headers has already been printed or not.

hasProjectAnnotation(AnnotationType, Annotation.Source, Project) - Method in class net.sf.basedb.core.AnnotationSet

Check if the annotation set contains an annotation of the specified type.

hasProjectSpecificAnnotation() - Method in class net.sf.basedb.clients.web.util.ProjectSpecificInfoFilter

Check if the project-specific flag is set.

hasPropertyFilter(String) - Method in class net.sf.basedb.core.ItemContext

Checks if there is a filter for the given property regardless of filter row.

hasPropertyLink - Variable in class net.sf.basedb.clients.web.ModeInfo

hasPropertyLink() - Method in class net.sf.basedb.clients.web.ModeInfo

hasRadio - Variable in class net.sf.basedb.clients.web.ModeInfo

hasRadio() - Method in class net.sf.basedb.clients.web.ModeInfo

hasReceived(Signal) - Method in class net.sf.basedb.core.signal.DelegatingSignalHandler

Check if the given signal has been received by this signal handler.

hasReceived(Signal) - Method in class net.sf.basedb.core.signal.EnhancedThreadSignalHandler

Check if the given signal has been received by this signal handler.

hasReceived(Signal) - Method in class net.sf.basedb.core.signal.ThreadSignalHandler

Check if the given signal has been received by this signal handler.

hasReceivedSignals() - Method in class net.sf.basedb.core.signal.DelegatingSignalHandler

Check if any signals has been received by this handler.

hasReceivedSignals() - Method in class net.sf.basedb.core.signal.EnhancedThreadSignalHandler

Check if any signals has been received by this handler.

hasReceivedSignals() - Method in class net.sf.basedb.core.signal.ProgressReporterSignalHandler

Check if any signals has been received by this handler.

hasRequiredAssayFields(BaseFileParser, FlatFileParser, List<String>) - Method in class net.sf.basedb.util.importer.spotdata.GenericIntensityParser

hasRequiredAssayFields(BaseFileParser, FlatFileParser, List<String>) - Method in class net.sf.basedb.util.importer.spotdata.MAParser

hasRequiredAssayFields(BaseFileParser, FlatFileParser, List<String>) - Method in interface net.sf.basedb.util.importer.spotdata.SpotIntensityParser

Check the list of assay fields to see if all columns that are required are present or not.

hasSignalTransporter() - Method in class net.sf.basedb.core.Job

Checks if a signal transporter has been registered for this job or not.

hasSingleParent() - Method in class net.sf.basedb.core.MeasuredBioMaterial

Checks if this biomaterial has a single parent item or not.

hasSshPrivateKey() - Method in class net.sf.basedb.core.FileServer

Check if a SSH private key has been set on this file server.

hasStickyHeaders() - Method in class net.sf.basedb.clients.web.taglib.table.Table

hasSubCategory() - Method in class net.sf.basedb.core.ItemContext

Is this context related to a given annotation type category or not?

hasSyncFilters() - Method in class net.sf.basedb.core.ItemList

Does this item list define any sync filters?

hasSystemPermission(Permission) - Method in class net.sf.basedb.core.SessionControl

Check if the logged in user has the specified system permission.

hasTable(VirtualTable) - Method in class net.sf.basedb.core.VirtualDb

Check if a real database table for this virtual database exists.

hasText - Variable in class net.sf.basedb.clients.web.taglib.table.Toolbar

If buttons should display text.

hasText() - Method in class net.sf.basedb.clients.web.taglib.table.Toolbar

hasTimedOut - Variable in class net.sf.basedb.util.uri.http.HttpConnectionManager.TimeoutTimer

hasTimedOut() - Method in class net.sf.basedb.util.uri.http.HttpConnectionManager.TimeoutTimer

hasTimePart(String) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil

hasToolbar - Variable in class net.sf.basedb.clients.web.ModeInfo

hasToolbar() - Method in class net.sf.basedb.clients.web.ModeInfo

hasUnit() - Method in class net.sf.basedb.core.Annotation

Checks if the values in this annotation has a unit.

hasValidFile() - Method in class net.sf.basedb.clients.web.extensions.ServletLoader

Checks if an XML file has passed validation in the ServletLoader.validateXmlFile(InputStream, String) method.

hasValidFile() - Method in class net.sf.basedb.util.extensions.xml.XmlLoader

Checks if an XML file has passed validation in the XmlLoader.validateXmlFile(InputStream, String) method.

having(Restriction) - Method in class net.sf.basedb.core.AbstractEntityQuery

Not supported.

having(Restriction) - Method in class net.sf.basedb.core.AbstractQuery

having(Restriction) - Method in interface net.sf.basedb.core.query.Query

Add a restriction query element to the having list.

HAVING - Enum constant in enum class net.sf.basedb.core.query.QuerySection

havingPermanent(Restriction) - Method in class net.sf.basedb.core.AbstractEntityQuery

Not supported.

havingPermanent(Restriction) - Method in class net.sf.basedb.core.AbstractQuery

havingPermanent(Restriction) - Method in interface net.sf.basedb.core.query.Query

Permanently add a restriction query element to the having list.

havings - Variable in class net.sf.basedb.core.AbstractQuery

List of having restrictions added to the query.

Head - Class in net.sf.basedb.clients.web.taglib

This tag defines the header section of a page.

Head() - Constructor for class net.sf.basedb.clients.web.taglib.Head

header - Variable in class net.sf.basedb.util.parser.FlatFileParser

The regular expression for matching a header line.

Header - Class in net.sf.basedb.clients.web.taglib.table

This tag defines a header column among the colummns or on a row.

Header() - Constructor for class net.sf.basedb.clients.web.taglib.table.Header

HEADER - Enum constant in enum class net.sf.basedb.util.parser.FlatFileParser.LineType

The parsed line is a header line, matching the regular expression specified by FlatFileParser.setHeaderRegexp(Pattern).

HEADER_EVENT - Static variable in class net.sf.basedb.util.bfs.AnnotationParser

Event type that is issued when the header line is found.

HEADER_REGEXP - Static variable in class net.sf.basedb.util.jobagent.JobAgentConnection

Regexp used to parse a typical answer.

headerLines - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter

headerPart - Variable in class net.sf.basedb.util.basefile.BaseFileWriter

headerRegexpParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter

Parameter definition that asks for the regular expression that splits a header line in key/value pair.

HeaderRow - Class in net.sf.basedb.clients.web.taglib.table

Container tag for a single header row in a table.

HeaderRow() - Constructor for class net.sf.basedb.clients.web.taglib.table.HeaderRow

headers - Variable in class net.sf.basedb.clients.web.taglib.table.Form

headers - Variable in class net.sf.basedb.core.data.RawBioAssayData

headers - Variable in class net.sf.basedb.util.bfs.AnnotationModel

headers - Variable in class net.sf.basedb.util.parser.FlatFileParser

Map of header lines parsed by the FlatFileParser.parseHeaders() method.

Headers - Class in net.sf.basedb.clients.web.taglib.table

Container tag for header rows in a table.

Headers() - Constructor for class net.sf.basedb.clients.web.taglib.table.Headers

height - Variable in class net.sf.basedb.clients.web.extensions.plot.MAPlotFactory

height - Variable in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean

height - Variable in class net.sf.basedb.core.data.AnnotationTypeData

height - Variable in class net.sf.basedb.core.ParameterType

Height of the input field for the parameter in the GUI.

help - Variable in class net.sf.basedb.clients.web.extensions.login.LoginFormBean

Help - Class in net.sf.basedb.clients.web.taglib

This tag is used to make it easier to add help features on a BASE web page.

Help - Class in net.sf.basedb.core

This class is used to represent a help text for a client application.

Help() - Constructor for class net.sf.basedb.clients.web.taglib.Help

Help(HelpData) - Constructor for class net.sf.basedb.core.Help

Creates a new help item

HELP - Enum constant in enum class net.sf.basedb.core.Item

The item is a Help.

HelpData - Class in net.sf.basedb.core.data

This class holds information about an help item.

HelpData() - Constructor for class net.sf.basedb.core.data.HelpData

helper - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn

helper - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper.CloseMyDbControl

HelpExporter - Class in net.sf.basedb.plugins

This plugin exports helptexts stored in the database to a XML-file.

HelpExporter() - Constructor for class net.sf.basedb.plugins.HelpExporter

helpid - Variable in class net.sf.basedb.clients.web.taglib.Help

The keyword of the helptopic

helpid - Variable in class net.sf.basedb.clients.web.taglib.tab.Tab

The help ID for this tab.

helpId - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory

helpId - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory

helpId - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean

HelpImporter - Class in net.sf.basedb.plugins

This plugin imports helptexts into database from a XML-file.

HelpImporter() - Constructor for class net.sf.basedb.plugins.HelpImporter

helpList - Static variable in class net.sf.basedb.plugins.HelpExporter

helpList - Static variable in class net.sf.basedb.plugins.HelpImporter

helpTexts - Variable in class net.sf.basedb.core.data.ClientData

hibernateType - Variable in class net.sf.basedb.core.hibernate.TypeWrapper

hibernateType - Variable in class net.sf.basedb.core.Metadata.BasicData2ItemPropertyPath

hibernateType - Variable in class net.sf.basedb.core.Metadata.BasicItem2DataPropertyPath

hibernateType - Variable in class net.sf.basedb.core.Metadata.CollectionPropertyPath

hibernateType - Variable in class net.sf.basedb.core.Metadata.ComponentPropertyPath

hibernateType - Variable in class net.sf.basedb.core.Metadata.DateCopyPropertyPath

hibernateType - Variable in class net.sf.basedb.core.Metadata.EntityPropertyPath

hibernateType - Variable in class net.sf.basedb.core.Metadata.EvictPropertyPath

hibernateType - Variable in class net.sf.basedb.core.Metadata.IdentifierPropertyPath

hibernateType - Variable in class net.sf.basedb.core.Metadata.MapPropertyPath

hibernateType - Variable in class net.sf.basedb.core.Metadata.NoopPropertyPath

hibernateType - Variable in class net.sf.basedb.core.Metadata.ReporterScore2DataPropertyPath

HibernateUtil - Class in net.sf.basedb.core

This class collects most of the functionality we need for using Hibernate.

HibernateUtil() - Constructor for class net.sf.basedb.core.HibernateUtil

HibernateUtil.DelayedFilterDef - Class in net.sf.basedb.core

HibernateUtil.FilterConfigurator - Class in net.sf.basedb.core

Helper class for defining filters at runtime.

hidden - Variable in class net.sf.basedb.core.ExtendedProperty

hidden - Variable in class net.sf.basedb.core.PluginParameter

If the parameter should be hidden from user input or not.

Hidden - Class in net.sf.basedb.clients.web.taglib.table

This tag defines a hidden input element that should be included in the form.

Hidden() - Constructor for class net.sf.basedb.clients.web.taglib.table.Hidden

HIDDEN_STRING - Enum constant in enum class net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType

hiddenCharacters - Variable in class net.sf.basedb.clients.web.extensions.login.FieldInfo

hiddenFilteredColumns - Variable in class net.sf.basedb.clients.web.taglib.table.Table

hiddenForm - Variable in class net.sf.basedb.clients.web.taglib.table.Table

hiddenMembers - Variable in class net.sf.basedb.core.data.GroupData

HideableSection - Class in net.sf.basedb.clients.web.taglib

This tag is used to display a section on a web page that can be shown/hidden by the user by clicking on an icon on it's title.

HideableSection() - Constructor for class net.sf.basedb.clients.web.taglib.HideableSection

hideClass - Variable in class net.sf.basedb.clients.web.taglib.HideableSection

hideClazz - Variable in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory

hideClazz - Variable in class net.sf.basedb.clients.web.extensions.section.SectionBean

high - Variable in class net.sf.basedb.core.query.BetweenRestriction

highExcludeParameter - Static variable in class net.sf.basedb.plugins.MedianRatioNormalization

highlight - Variable in class net.sf.basedb.clients.web.taglib.table.Row

Optional class attribute that is applied when the mouse is over the current row.

highValue - Variable in class net.sf.basedb.core.AnnotationBetweenRestriction

hilo - Variable in class net.sf.basedb.util.plot.HistogramPlot

HILOMAXMIN - Enum constant in enum class net.sf.basedb.util.plot.HistogramPlot.YAggregate

Plot a high/low bar for each bin with the maximum and minimum values.

HILOSTDEV - Enum constant in enum class net.sf.basedb.util.plot.HistogramPlot.YAggregate

Plot a high/low bar for each bin with the mean +/- 1 standard deviation.

histogram - Variable in class net.sf.basedb.util.plot.HistogramPlot

HistogramBin(float, float) - Constructor for class net.sf.basedb.util.plot.HistogramPlot.HistogramBin

Create a new HistogramBin.

HistogramDataset() - Constructor for class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset

HistogramPlot - Class in net.sf.basedb.util.plot

A simple plot utility for generating histogram plots without the need to delve deep into the JFreePlot package.

HistogramPlot(String, String, XYItemRenderer) - Constructor for class net.sf.basedb.util.plot.HistogramPlot

Create a new HistogramPlot.

HistogramPlot.HistogramBin - Class in net.sf.basedb.util.plot

Represents a single bin in a histogram.

HistogramPlot.HistogramDataset - Class in net.sf.basedb.util.plot

An dataset implementation for histogram data that allows us to send data to JFreeChart the way we want.

HistogramPlot.HistogramSeries - Class in net.sf.basedb.util.plot

Collects information about one histogram series.

HistogramPlot.TempSeries - Class in net.sf.basedb.util.plot

Helper class for storing histogram data that needs to split into different annotations.

HistogramPlot.YAggregate - Enum Class in net.sf.basedb.util.plot

Defines what to to plot on the y axis in a histogram plot.

HistogramSeries(String, float[], float[], float, HistogramPlot.YAggregate, float, float) - Constructor for class net.sf.basedb.util.plot.HistogramPlot.HistogramSeries

Create a new HistogramSeries.

HistogramSeries(String, HistogramPlot.HistogramSeries, HistogramPlot.YAggregate) - Constructor for class net.sf.basedb.util.plot.HistogramPlot.HistogramSeries

Create a new HistogramSeries that is using data from another series.

history - Variable in class net.sf.basedb.core.data.ChangeHistoryDetailData

history - Variable in class net.sf.basedb.core.log.db.DbLogManager

HOLDER - Static variable in class net.sf.basedb.core.AbstractQuery

holders - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter

home - Variable in class net.sf.basedb.util.extensions.xml.PathConverter

HOME - Static variable in class net.sf.basedb.core.Directory

The id for the Directory item representing the home directory.

homeDirectory - Variable in class net.sf.basedb.core.data.UserData

host - Variable in class net.sf.basedb.clients.web.servlet.RssNewsFeed

host - Variable in class net.sf.basedb.core.data.FileServerData

host - Variable in class net.sf.basedb.util.uri.ConnectionParameters

hostName - Static variable in class net.sf.basedb.core.Application

The host name of the server running BASE.

hostName - Static variable in class net.sf.basedb.util.EmailUtil

hostPort - Static variable in class net.sf.basedb.util.EmailUtil

Hql - Class in net.sf.basedb.core.query

A factory class to create expressions, joins, etc. that are only used by HQL queries.

Hql() - Constructor for class net.sf.basedb.core.query.Hql

HQL - Enum constant in enum class net.sf.basedb.core.query.QueryType

The query is using Hibernate Query Language.

HqlElementsExpression - Class in net.sf.basedb.core.query

An expression representing the elements collection of a collection of a Hibernate entity: elements(alias.property).

HqlElementsExpression(String, String) - Constructor for class net.sf.basedb.core.query.HqlElementsExpression

HqlEntityExpression - Class in net.sf.basedb.core.query

An expression representing a Hibernate entity.

HqlEntityExpression(BasicItem) - Constructor for class net.sf.basedb.core.query.HqlEntityExpression

HqlEntityExpression(BasicData) - Constructor for class net.sf.basedb.core.query.HqlEntityExpression

HqlEntityParameterExpression - Class in net.sf.basedb.core.query

Entity parameter expression.

HqlEntityParameterExpression(String, Item) - Constructor for class net.sf.basedb.core.query.HqlEntityParameterExpression

HqlExpression - Class in net.sf.basedb.core.query

A class holding an expression or a restriction where a prefix can be used to represent a root alias in a HQL.

HqlExpression(String, String) - Constructor for class net.sf.basedb.core.query.HqlExpression

HqlIndexExpression - Class in net.sf.basedb.core.query

An expression representing the index collection of a map or list of a Hibernate entity: index(alias.property)

HqlIndexExpression(String, String) - Constructor for class net.sf.basedb.core.query.HqlIndexExpression

HqlInnerJoin - Class in net.sf.basedb.core.query

Inner joins an association to another item: JOIN <alias.property> <joinedAlias> to the query.

HqlInnerJoin(String, String, String, Restriction, boolean) - Constructor for class net.sf.basedb.core.query.HqlInnerJoin

HqlLeftJoin - Class in net.sf.basedb.core.query

Left joins an association to another item: LEFT JOIN <alias.property> <joinedAlias> to the query.

HqlLeftJoin(String, String, String, Restriction, boolean) - Constructor for class net.sf.basedb.core.query.HqlLeftJoin

hqlMode - Variable in class net.sf.basedb.core.query.ReporterListExpression

HqlPropertyExpression - Class in net.sf.basedb.core.query

An expression representing the property of a Hibernate entity: alias.property or alias.property[index]

HqlPropertyExpression(String, String, Expression) - Constructor for class net.sf.basedb.core.query.HqlPropertyExpression

HqlQuery - Interface in net.sf.basedb.core.query

This is a query that is using HQL (Hibernate Query Language) as the query language.

HqlQueryJoiners - Class in net.sf.basedb.core

This class collects AutoJoiner:s for HqlQuery queries.

HqlQueryJoiners() - Constructor for class net.sf.basedb.core.HqlQueryJoiners

HqlQueryJoiners.AnnotationJoiner - Class in net.sf.basedb.core

Joiner for annotations.

HqlQueryJoiners.ReporterListJoiner - Class in net.sf.basedb.core

Joiner for reporter lists.

HqlRightJoin - Class in net.sf.basedb.core.query

Right joins an association to another item: RIGHT JOIN <alias.property> <joinedAlias> to the query.

HqlRightJoin(String, String, String, Restriction) - Constructor for class net.sf.basedb.core.query.HqlRightJoin

HqlSizeExpression - Class in net.sf.basedb.core.query

An expression representing the size of the of a collection of a Hibernate entity: size(alias.property).

HqlSizeExpression(String, String) - Constructor for class net.sf.basedb.core.query.HqlSizeExpression

href - Variable in class net.sf.basedb.clients.web.taglib.Icon

If present, the icon is enclosed with an <a> tag that opens the given url in a new window.

href - Variable in class net.sf.basedb.clients.web.taglib.path.PathElement

URL to the linked page.

hSession - Variable in class net.sf.basedb.core.DbControl.State

hStatelessSession - Variable in class net.sf.basedb.core.DbControl.State

HTML - Class in net.sf.basedb.clients.web.util

This class contains a set of static methods that may be useful in a web application for handling text/HTML strings.

HTML() - Constructor for class net.sf.basedb.clients.web.util.HTML

hTransaction - Variable in class net.sf.basedb.core.DbControl.State

HTTP_DATE_FORMAT - Static variable in class net.sf.basedb.util.HttpUtil

HttpConnectionManager - Class in net.sf.basedb.util.uri.http

Connection manager implementation that support HTTP and HTTPS URI:s.

HttpConnectionManager(URI, ConnectionParameters) - Constructor for class net.sf.basedb.util.uri.http.HttpConnectionManager

HttpConnectionManager.TimeoutTimer - Class in net.sf.basedb.util.uri.http

HttpConnectionManagerActionFactory - Class in net.sf.basedb.util.uri.http

Action factory for http connection manager factory.

HttpConnectionManagerActionFactory() - Constructor for class net.sf.basedb.util.uri.http.HttpConnectionManagerActionFactory

HttpConnectionManagerFactory - Class in net.sf.basedb.util.uri.http

Connection manager factory for HTTP and HTTPS URI:s.

HttpConnectionManagerFactory() - Constructor for class net.sf.basedb.util.uri.http.HttpConnectionManagerFactory

Create a new http connection manager factory.

HttpUtil - Class in net.sf.basedb.util

Useful methods related to HTTP stuff in general and Apache HTTP components in particular.

HttpUtil() - Constructor for class net.sf.basedb.util.HttpUtil

hybQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

HYBRIDIZATION - Static variable in class net.sf.basedb.core.Kit

The ID for the hybridization kit type, for example a kit used when creating a PhysicalBioAssay from a set of (labeled) Extract:s.

HYBRIDIZATION - Static variable in class net.sf.basedb.core.PhysicalBioAssay

The id for the PhysicalBioAssayType item representing a hybridization.

HYBRIDIZATION - Static variable in class net.sf.basedb.core.Protocol

The ID for the hybridization protocol type, for example a protocol used when creating a PhysicalBioAssay from a set of (labeled) Extract:s.

HYBRIDIZATION_STATION - Static variable in class net.sf.basedb.core.Hardware

The id for the HardwareType object representing a hybridization station.

I

icon - Variable in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

icon - Variable in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean

icon - Variable in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean

icon - Variable in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory

icon - Variable in class net.sf.basedb.clients.web.taglib.menu.Menuitem

An icon to display.

icon - Variable in class net.sf.basedb.clients.web.taglib.menu.Submenu

An icon to display.

icon - Variable in enum class net.sf.basedb.util.extensions.logging.LogLevel

Icon - Class in net.sf.basedb.clients.web.taglib

This tag is used to make it easier to display icons on a BASE web page.

Icon() - Constructor for class net.sf.basedb.clients.web.taglib.Icon

id - Variable in class net.sf.basedb.clients.jobagent.slotmanager.Slot

id - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup

id - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.ReporterPositions

id - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

id - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

id - Variable in class net.sf.basedb.clients.web.extensions.login.LoginFormBean

id - Variable in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

id - Variable in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean

id - Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

id - Variable in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean

id - Variable in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean

id - Variable in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory

id - Variable in class net.sf.basedb.clients.web.extensions.section.SectionBean

id - Variable in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory

id - Variable in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory

id - Variable in class net.sf.basedb.clients.web.extensions.startpage.StartPageBean

id - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory

id - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory

id - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean

id - Variable in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean

id - Variable in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory

id - Variable in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

id - Variable in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey

id - Variable in class net.sf.basedb.clients.web.taglib.table.TableColumn

id - Variable in class net.sf.basedb.core.data.annotations.AnnotationLink

id - Variable in class net.sf.basedb.core.data.BasicData

id - Variable in class net.sf.basedb.core.ItemProxy

id - Variable in class net.sf.basedb.core.ParameterValuesImpl

The id of the job or configuration.

id - Variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager.AnnotationInfo

id - Variable in class net.sf.basedb.core.query.HqlEntityExpression

id - Variable in class net.sf.basedb.core.RawDataBatcher.FeatureProxy

id - Variable in class net.sf.basedb.core.RawDataBatcher.ReporterProxy

id - Variable in class net.sf.basedb.core.RawDataType

id - Variable in class net.sf.basedb.core.SessionControl.ClientInfo

id - Variable in class net.sf.basedb.core.SessionControl

The id of the object.

id - Variable in class net.sf.basedb.core.signal.Signal

id - Variable in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField

id - Variable in class net.sf.basedb.plugins.BfsExporterPlugin.ExtendedExportableField

id - Variable in class net.sf.basedb.util.bfs.EventType

id - Variable in class net.sf.basedb.util.extensions.events.ExtensionEventFilter

id - Variable in class net.sf.basedb.util.extensions.events.ExtensionPointEventFilter

id - Variable in class net.sf.basedb.util.extensions.ExtensionBean

id - Variable in class net.sf.basedb.util.extensions.ExtensionPointBean

id - Variable in class net.sf.basedb.util.extensions.manager.ExtensionKey

id - Variable in class net.sf.basedb.util.extensions.manager.ExtensionPointKey

id - Variable in class net.sf.basedb.util.extensions.Registry.AttributeKey

id - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtension

id - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint

id - Variable in class net.sf.basedb.util.extensions.SingleExtensionFilter

id - Variable in class net.sf.basedb.util.extensions.xml.PluginInfo

id - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileImporter.RawDataProxy

id - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileImporter.ReporterProxy

id - Variable in class net.sf.basedb.util.importer.spotdata.ExtraFloatParser

id - Variable in class net.sf.basedb.util.overview.Validator

id - Variable in class net.sf.basedb.util.uri.http.HttpConnectionManagerFactory

ID - Static variable in class net.sf.basedb.core.ClonableProperty

The property name of the "static" property BasicData.getId().

idAnnotationColumnMapping - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

Column mapping parameter for the annotation column used for item identification.

idAnnotationColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Column mapping parameter for the annotation column used for item identification.

idColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

Identifiable - Interface in net.sf.basedb.core

An Identifiable item is an item which has an id a type and a version.

IdentifiableData - Interface in net.sf.basedb.core.data

An identifiable item is an item which has an id and a version.

IdentifiableFormatter - Class in net.sf.basedb.util.formatter

Formatter to handle Identifiable items.

IdentifiableFormatter() - Constructor for class net.sf.basedb.util.formatter.IdentifiableFormatter

Create a new formatter.

IdentifiableFormatter(String) - Constructor for class net.sf.basedb.util.formatter.IdentifiableFormatter

Create a new formatter.

identificationSection - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

identificationSection - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

identificationSection - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

IdentifierPropertyPath(Type) - Constructor for class net.sf.basedb.core.Metadata.IdentifierPropertyPath

IdentityConverter<T> - Class in net.sf.basedb.util.json

Simple "converter" implementation that simply return the same object.

IdentityConverter() - Constructor for class net.sf.basedb.util.json.IdentityConverter

IdentityEncoderDecoder - Class in net.sf.basedb.util.encode

Encoder decoder implementation that doesn't encode or decode anything.

IdentityEncoderDecoder() - Constructor for class net.sf.basedb.util.encode.IdentityEncoderDecoder

IdentityFilter<T> - Class in net.sf.basedb.util.filter

A filter implementation that only accepts an object if it is identical (==) to a given object.

IdentityFilter(T) - Constructor for class net.sf.basedb.util.filter.IdentityFilter

Create a new filter.

IdentityScaleFactor() - Constructor for class net.sf.basedb.util.InputStreamTracker.IdentityScaleFactor

IdentityUnitConverter - Class in net.sf.basedb.util.units

A unit "converter" that doesn't modify the values.

IdentityUnitConverter() - Constructor for class net.sf.basedb.util.units.IdentityUnitConverter

Create a new unit converter.

idExpression - Variable in class net.sf.basedb.core.query.IdListRestriction

idList - Variable in class net.sf.basedb.core.query.IdListRestriction

idList(DbControl) - Method in class net.sf.basedb.core.AbstractEntityQuery

idList(DbControl) - Method in interface net.sf.basedb.core.query.EntityQuery

Execute the query and return the ID values of all items matching the query.

IdListRestriction - Class in net.sf.basedb.core.query

Restriction that filters on a list of ID values: id IN (a, b, c, ....)

IdListRestriction() - Constructor for class net.sf.basedb.core.query.IdListRestriction

IdListRestriction(boolean) - Constructor for class net.sf.basedb.core.query.IdListRestriction

IdListRestriction(boolean, Set<Integer>) - Constructor for class net.sf.basedb.core.query.IdListRestriction

IdListRestriction(String, boolean, Collection<Integer>) - Constructor for class net.sf.basedb.core.query.IdListRestriction

IdListRestriction(String, Collection<Integer>) - Constructor for class net.sf.basedb.core.query.IdListRestriction

IdListRestriction(Set<Integer>) - Constructor for class net.sf.basedb.core.query.IdListRestriction

idMapper - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

idMapper - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

idMapper - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

idMapping - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

idMapping - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

idMethod - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

idMethod - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

idMethod - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

IdMethod - Interface in net.sf.basedb.plugins.batchimport

Represents an 'identification method', eg. a way to find an item among the items that already exists in the database.

idPropertyName - Variable in class net.sf.basedb.core.BasicBatcher

The name of the ID property.

IfConverter - Class in net.sf.basedb.util.jep.convert

Convert If function to a Query API Expression.

IfConverter() - Constructor for class net.sf.basedb.util.jep.convert.IfConverter

ifFalse - Variable in class net.sf.basedb.core.query.ConditionalQueryElement

ifFound - Variable in class net.sf.basedb.util.charset.SimpleStringDetector

ifTrue - Variable in class net.sf.basedb.core.query.ConditionalQueryElement

ignore - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsManager

ignore - Variable in class net.sf.basedb.util.parser.FlatFileParser

The regular expression for matching a comment line.

IGNORE - Enum constant in enum class net.sf.basedb.util.overview.Severity

The rule is ignored.

ignoreActiveProject - Variable in class net.sf.basedb.core.Annotation

ignoreAllErrors - Variable in class net.sf.basedb.util.error.SimpleErrorHandler

ignored - Static variable in class net.sf.basedb.clients.web.PermissionUtil

All items which permissions depend on some other item only.

IGNORED - Enum constant in enum class net.sf.basedb.util.parser.FlatFileParser.LineType

The parsed line was ignored since it matched the regular expression specified by FlatFileParser.setIgnoreRegexp(Pattern).

ignoredFiles - Variable in class net.sf.basedb.util.extensions.manager.Settings

ignoredLines - Variable in class net.sf.basedb.util.parser.FlatFileParser

Number of ignored lines in the FlatFileParser.nextData() method.

ignoredSql - Variable in class net.sf.basedb.core.hibernate.SchemaGenerator

ignoreErrorFlag - Variable in class net.sf.basedb.clients.web.extensions.InstallFilter

ignoreFilename - Variable in class net.sf.basedb.util.FileExportOutputStream

IgnoreFileProcessor - Class in net.sf.basedb.util.extensions.manager.processor

Processor implementation for ignoring files.

IgnoreFileProcessor(ProcessResults) - Constructor for class net.sf.basedb.util.extensions.manager.processor.IgnoreFileProcessor

IgnoreFilter - Class in net.sf.basedb.clients.web.extensions

Filter implementation that selects only those extensions that was selected for ignoring by the user in the gui.

IgnoreFilter(HttpServletRequest) - Constructor for class net.sf.basedb.clients.web.extensions.IgnoreFilter

ignoreNonExistingColumns - Variable in class net.sf.basedb.util.parser.ColFunction

ignoreNonExistingColumns - Variable in class net.sf.basedb.util.parser.FlatFileParser

If non-existing columns should be ignored (true) or result in an exception (false)

ignoreNotFoundItems - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

ignoreRegexpParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter

Parameter definition that asks for the regular expression that matches a line that should be ignored.

ignoreSubtypeFilter - Variable in class net.sf.basedb.core.ItemContext

ignoreUseInternalJobQueueFlag - Variable in class net.sf.basedb.core.InternalJobQueue

If the PluginDefinitionData.getUseInternalJobQueue() setting should be ignored or not.

illumina - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter

IlluminaRawDataImporter - Class in net.sf.basedb.plugins

An importer plug-in for Illumina raw data.

IlluminaRawDataImporter() - Constructor for class net.sf.basedb.plugins.IlluminaRawDataImporter

IlluminaRawDataImporter.BatchAndMapHolder - Class in net.sf.basedb.plugins

Holds a RawBioAssay and the RawDataBatcher to use for import and the Mapper for all it's data columns.

image - Variable in class net.sf.basedb.clients.web.taglib.Button

The image to display.

image - Variable in class net.sf.basedb.clients.web.taglib.Help

The path to the help icon

image - Variable in class net.sf.basedb.clients.web.taglib.Icon

The filename of the image.

image - Variable in class net.sf.basedb.clients.web.taglib.table.Button

An optional image to show in the button.

image - Variable in class net.sf.basedb.clients.web.taglib.table.Label

An optional image to show in the button.

image - Variable in class net.sf.basedb.clients.web.taglib.Zoom

The path to the help icon

image - Variable in class net.sf.basedb.core.data.PlateMappingData

IMAGE - Static variable in class net.sf.basedb.core.File

The id for the FileType item representing an image file.

IMAGE_EXTENSION - Static variable in class net.sf.basedb.clients.web.util.HTML

ImageRemapFilter - Class in net.sf.basedb.clients.web.servlet

This is a filter that remaps request to images to some other image.

ImageRemapFilter() - Constructor for class net.sf.basedb.clients.web.servlet.ImageRemapFilter

ImageRemapper - Class in net.sf.basedb.clients.web.extensions.skin

Remaps image URLs.

ImageRemapper() - Constructor for class net.sf.basedb.clients.web.extensions.skin.ImageRemapper

Creates a new image remapper.

ImageRemapperUtil - Class in net.sf.basedb.clients.web.extensions.skin

Utility class for working with image remapping.

ImageRemapperUtil() - Constructor for class net.sf.basedb.clients.web.extensions.skin.ImageRemapperUtil

ImmediateDownloadExporter - Interface in net.sf.basedb.core.plugin

This interface should be implemented by export plugins that supports immediate download to the client application.

impersonated - Variable in class net.sf.basedb.core.data.SessionData

impersonated - Variable in class net.sf.basedb.core.SessionControl.LoginInfo

If the logged in user was logged in with the SessionControl.impersonateLogin(int, String)

impersonateLogin(int, String) - Method in class net.sf.basedb.core.PluginSessionControl

impersonateLogin(int, String) - Method in class net.sf.basedb.core.SessionControl

Log in as another user or create a clone of the currently logged in user's session.

impersonateLogin(Ownable, String) - Method in class net.sf.basedb.core.SessionControl

Log in as the owner of the specified item.

IMPORT - Enum constant in enum class net.sf.basedb.core.plugin.Plugin.MainType

importableFileTypes - Variable in class net.sf.basedb.plugins.ManualTransformCreator

importAll - Variable in class net.sf.basedb.plugins.PluginConfigurationImporter

importAll(String, ProgressReporter) - Static method in class net.sf.basedb.core.Migration

Import data to a BASE database.

importAllParameter - Static variable in class net.sf.basedb.plugins.PluginConfigurationImporter

importData(DbControl, File, Transformation, IntensityTransform, ProgressReporter) - Method in class net.sf.basedb.plugins.Base1PluginExecuter

Imports the data from the file stdout.txt in the execution directory.

importer - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

importExtraFile(String, InputStreamLocator) - Method in interface net.sf.basedb.util.bfs.ExtraFileImporter

Import the file data into a file in the BASE file system.

importExtraFile(String, InputStreamLocator) - Method in class net.sf.basedb.util.bfs.GenericExtraFileImporter

importFromCdf(DbControl, FusionCDFData, ProgressReporter) - Method in class net.sf.basedb.plugins.CdfFileReporterImporter

importFromFile(TableInfo, File, File, DbEngine, Statement, ProgressReporter) - Method in class net.sf.basedb.core.Migration

Import data to the given table.

ImportInputStream - Class in net.sf.basedb.core.plugin

An input stream used for input to import plug-ins.

ImportInputStream(InputStream) - Constructor for class net.sf.basedb.core.plugin.ImportInputStream

Create a new import stream.

importPluginConfigurationsFromJar(String, String, HashMap<Integer, Boolean>, boolean, boolean) - Method in class net.sf.basedb.plugins.PluginConfigurationImporter

Imports plugin configurations direct from an xml file, located in a jar.

importTempFiles(DbControl, File[], Directory) - Method in class net.sf.basedb.plugins.Base1PluginExecuter

in - Variable in class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor.StreamRedirector

in - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.InExpression

in - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload

The stream coming from the browser.

in - Variable in class net.sf.basedb.plugins.LowessNormalization.CallableWorker

in - Variable in class net.sf.basedb.util.bfs.AnnotationParser

in - Variable in class net.sf.basedb.util.bfs.DataParser

in - Variable in class net.sf.basedb.util.bfs.MetadataParser

in - Variable in class net.sf.basedb.util.FileCopyRunnable

in - Variable in class net.sf.basedb.util.InputStreamCombiner

in - Variable in class net.sf.basedb.util.InputStreamSplitter

The source input stream to read from.

in - Variable in class net.sf.basedb.util.InputStreamTracker

The source input stream to read from.

in(Expression, Expression...) - Static method in class net.sf.basedb.core.query.Restrictions

Check if an expression is contained in a set of other expressions: e1 IN (e2[0], e2[1], ...)

in(Expression, Query) - Static method in class net.sf.basedb.core.query.Restrictions

Create a subquery restriction: e1 IN (subquery).

IN - Enum constant in enum class net.sf.basedb.core.Operator

IN_PROJECT - Enum constant in enum class net.sf.basedb.core.Include

Include items in the active project.

inactive - Variable in class net.sf.basedb.core.data.KitData

inactiveColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.KitImporter

Column mapping parameter for the kit inactive flag.

inactiveMapper - Variable in class net.sf.basedb.plugins.batchimport.KitImporter

inactiveRoles - Variable in class net.sf.basedb.core.Keyring

Holds the ID of the roles that are inactive.

include - Variable in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory

include - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory

include - Variable in class net.sf.basedb.core.data.ContextData

include - Variable in class net.sf.basedb.core.data.ItemListSyncFilterData

include - Variable in class net.sf.basedb.core.ItemContext

include - Variable in class net.sf.basedb.util.listable.TransformContext

include(Collection<Include>) - Method in class net.sf.basedb.core.AbstractEntityQuery

include(Collection<Include>) - Method in interface net.sf.basedb.core.query.EntityQuery

include(Include...) - Method in class net.sf.basedb.core.AbstractEntityQuery

include(Include...) - Method in interface net.sf.basedb.core.query.EntityQuery

Specify options for which items to include in the result.

Include - Enum Class in net.sf.basedb.core

This enumeration defines constants that are used to specify which items to include in a query.

Include(int) - Constructor for enum class net.sf.basedb.core.Include

Constructor for Permission enums.

includeChildBioAssays - Variable in class net.sf.basedb.util.listable.CollectedExtractsToDerivedBioAssayTransformer

includeChildrenThatPushToParent - Variable in class net.sf.basedb.util.listable.ToExtractSourceItemTransformerFactory

includeChildrenThatPushToParent - Variable in class net.sf.basedb.util.listable.ToSampleSourceItemTransformerFactory

IncludeContentSectionFactory - Class in net.sf.basedb.clients.web.extensions.section

A section action factory implementation that includes another resource as the content of a section.

IncludeContentSectionFactory() - Constructor for class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory

Create a new factory instance.

IncludeContentSectionFactory.Section - Class in net.sf.basedb.clients.web.extensions.section

IncludeContentTabFactory - Class in net.sf.basedb.clients.web.extensions.tabcontrol

A tab action factory implementation that includes another resource as the content of tab.

IncludeContentTabFactory() - Constructor for class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory

Create a new factory instance.

IncludeContentTabFactory.Tab - Class in net.sf.basedb.clients.web.extensions.tabcontrol

includeDefault - Variable in class net.sf.basedb.core.FastAnnotationLoader

IncludeExcludeFilter - Class in net.sf.basedb.util

IncludeExcludeFilter(DbControl, BioAssaySet, List<BioAssay>, Restriction, Integer, Integer) - Constructor for class net.sf.basedb.util.IncludeExcludeFilter

includeInherited - Variable in class net.sf.basedb.core.AnnotationRestriction.Options

includeInherited() - Method in class net.sf.basedb.core.AnnotationRestriction.Options

Should inherited annotations be included in the search or not.

includeLimit - Variable in class net.sf.basedb.util.IncludeExcludeFilter

includePrimary - Variable in class net.sf.basedb.core.AnnotationRestriction.Options

includePrimary() - Method in class net.sf.basedb.core.AnnotationRestriction.Options

Should primary annotations be included in the search or not.

includes - Variable in class net.sf.basedb.core.AbstractEntityQuery

Flags specifying which items to include.

includes - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

includeSource - Variable in class net.sf.basedb.util.listable.CollectExtracts.CollectChildren

includeSource - Variable in class net.sf.basedb.util.listable.CollectExtracts.CollectParents

includeSourcesInTarget - Variable in class net.sf.basedb.util.listable.DerivedBioAssayToChildDerivedBioAssayTransformer

includeSourcesInTarget - Variable in class net.sf.basedb.util.listable.DerivedBioAssayToParentDerivedBioAssayTransformer

includeSourcesInTarget - Variable in class net.sf.basedb.util.listable.ExtractToChildExtractTransformer

includeSourcesInTarget - Variable in class net.sf.basedb.util.listable.ExtractToParentExtractTransformer

includeSourcesInTarget - Variable in class net.sf.basedb.util.listable.SampleToChildSampleTransformer

includeSourcesInTarget - Variable in class net.sf.basedb.util.listable.SampleToParentSampleTransformer

includeSpot(SqlResult) - Method in interface net.sf.basedb.util.DynamicFilter

Check if a spot should be included in the filtered output or not.

includeSpot(SqlResult) - Method in class net.sf.basedb.util.IncludeExcludeFilter

Check if a spot should be included in the filtered output or not.

inclusive - Variable in class net.sf.basedb.core.query.BetweenRestriction

incoming - Variable in class net.sf.basedb.util.jobagent.JobAgentServerConnection.RequestHandlerThread

INCORRECT_BIOASSAY_POSITION - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if the position of an extract on a physical bioassay is between 1 and the size of the bioassay.

INCORRECT_BIOMATERIAL_TYPE - Static variable in class net.sf.basedb.util.overview.Validator

Validator that checks if the biomaterial on a bioplate is of the correct item type.

INCORRECT_BIOSOURCE_TYPE - Static variable in class net.sf.basedb.util.overview.Validator

Validator that checks if the parent biosource of a sample has the expected subtype.

INCORRECT_DERIVEDBIOASSAY_TYPE - Static variable in class net.sf.basedb.util.overview.Validator

Validator that checks if a derived bioassay has the expected subtype.

INCORRECT_EXTRACT_TYPE - Static variable in class net.sf.basedb.util.overview.Validator

Validator that checks if the parent extract of a extract/bioassay has the expected subtype.

INCORRECT_FILETYPE - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if the file attached to an item has a correct file type.

INCORRECT_HARDWARETYPE - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if the hardware attached to an item has a correct hardware type.

INCORRECT_KITTYPE - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if the kit attached to an item has a correct kit type.

INCORRECT_PHYSICALBIOASSAY_TYPE - Static variable in class net.sf.basedb.util.overview.Validator

Validator that checks if a physical bioassay has the expected subtype.

INCORRECT_PROTOCOLTYPE - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if the protocol attached to an item has a correct protocol type.

INCORRECT_SAMPLE_TYPE - Static variable in class net.sf.basedb.util.overview.Validator

Validator that checks if the parent sample of a sample/extract has the expected subtype.

INCORRECT_SOFTWARETYPE - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if the software attached to an item has a correct software type.

INCORRECT_TAGTYPE - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if the tag attached to an extract has a correct subtype.

increaseCount() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin

Increase the count value in this bin.

increaseSectionCount(String, int) - Method in class net.sf.basedb.util.basefile.BaseFileParser

Counts the number of times a section has been seen in the file.

index - Variable in class net.sf.basedb.clients.web.extensions.list.AnyLinkColumn

index - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn

index - Variable in class net.sf.basedb.core.data.BioPlateEventParticipantData

index - Variable in class net.sf.basedb.core.Metadata.ComponentPropertyPath

index - Variable in class net.sf.basedb.core.migrate.AbstractResultWriter

index - Variable in class net.sf.basedb.core.query.HqlPropertyExpression

index - Variable in class net.sf.basedb.util.ArrayIterator

The index of the next element to return.

index - Variable in class net.sf.basedb.util.extensions.ExtensionBean

index - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtension

index - Variable in class net.sf.basedb.util.gtf.GtfInputStream

index - Variable in class net.sf.basedb.util.importer.spotdata.GenericIntensityParser

index - Variable in class net.sf.basedb.util.InputStreamCombiner

index - Variable in class net.sf.basedb.util.NestedIterator

The index of the next collection to return.

index - Variable in class net.sf.basedb.util.overview.cache.IndexedCacheKey

index - Variable in class net.sf.basedb.util.parser.ColumnMapper

index(String, String) - Static method in class net.sf.basedb.core.query.Hql

Create an index expression for a property that is a map or a list.

index_64 - Static variable in class net.sf.basedb.util.bcrypt.BCrypt

INDEX_COMPARATOR_CTX - Static variable in class net.sf.basedb.util.extensions.DefaultFilter

Comparator used to order a list of invokation contexts by the index value of the extension.

INDEX_COMPARATOR_EXT - Static variable in class net.sf.basedb.util.extensions.DefaultFilter

Comparator used to order a list of extensions by the index value of the extension.

indexColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.ArraySlideImporter

indexed - Variable in class net.sf.basedb.core.VirtualColumn

If the column should be indexed or not.

INDEXED - Static variable in class net.sf.basedb.core.VirtualColumn

Used in constructor to tell that the column should be indexed.

IndexedCacheKey - Class in net.sf.basedb.util.overview.cache

Cache key implementation that bundles another cache key with an index.

IndexedCacheKey(Object, int) - Constructor for class net.sf.basedb.util.overview.cache.IndexedCacheKey

IndexedCacheKey(Object, BasicItem) - Constructor for class net.sf.basedb.util.overview.cache.IndexedCacheKey

Create a cache key using the id of the BasicItem as the index.

indexes - Variable in class net.sf.basedb.core.dbengine.TableInfo

IndexInfo(String, boolean) - Constructor for class net.sf.basedb.core.dbengine.TableInfo.IndexInfo

Create a new IndexInfo object.

indexMapper - Variable in class net.sf.basedb.plugins.batchimport.ArraySlideImporter

indexOf(Object) - Method in class net.sf.basedb.core.ItemResultList

InExpression(int...) - Constructor for class net.sf.basedb.clients.web.ExperimentExplorer.InExpression

InExpression(Collection<? extends Number>) - Constructor for class net.sf.basedb.clients.web.ExperimentExplorer.InExpression

info - Variable in class net.sf.basedb.core.PluginDefinition

info - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil.CellTypeWithInfo

info - Variable in class net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser

info - Variable in class net.sf.basedb.util.importer.spotdata.SecondPassSectionSpotsParser

info - Variable in class net.sf.basedb.util.importer.spotdata.SectionAssaysParser

info - Variable in class net.sf.basedb.util.importer.spotdata.SectionReporterListParser

info(String) - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLogger

Log an INFO message.

info(String, Throwable) - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLogger

Log an INFO message with an optional stacktrace.

INFO - Enum constant in enum class net.sf.basedb.util.extensions.logging.LogLevel

INFO - Enum constant in enum class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory.Level

InfoRequestHandler - Class in net.sf.basedb.clients.jobagent.handlers

This is a request handler for the info and status commands.

InfoRequestHandler(Agent) - Constructor for class net.sf.basedb.clients.jobagent.handlers.InfoRequestHandler

inheritAll(AnnotationSet, boolean) - Method in class net.sf.basedb.core.AnnotationSet

Utility method for inheriting or cloning all annotations from the given annotation set.

inheritAnnotation(Annotation, boolean) - Method in class net.sf.basedb.core.AnnotationSet

Inherit or clone an annotation.

InheritAnnotationsManager - Class in net.sf.basedb.util.annotations

Manager class for batch inheriting of annotations.

InheritAnnotationsManager(DbControl, SnapshotManager, List<InheritSpecification>) - Constructor for class net.sf.basedb.util.annotations.InheritAnnotationsManager

InheritAnnotationsManager.AnnotationTypeFilter - Class in net.sf.basedb.util.annotations

Filter for finding annotation types to process.

InheritAnnotationsManager.UsableParentFilter - Class in net.sf.basedb.util.annotations

Filter used to find parent items that are annotated and for which the current user has permission to USE the annotations.

INHERITED - Enum constant in enum class net.sf.basedb.core.Annotation.Source

The annotation is an inherited annotation without a local copy of the values.

inheritedCreated(int, int, int, int, int, int) - Method in class net.sf.basedb.core.ProjectSpecificAnnotationsManager

An INHERITED/CLONED annotation has been created in this transaction.

inheritedFrom - Variable in class net.sf.basedb.core.data.AnnotationData

inheritedFrom - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot

inheritedFromId - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot

inheritedFromSetId - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot

inheritingAnnotations - Variable in class net.sf.basedb.core.data.AnnotationData

InheritSpecification - Class in net.sf.basedb.util.annotations

Class for holding rules for how annotations should be inherited from parent items.

InheritSpecification(AnnotationType) - Constructor for class net.sf.basedb.util.annotations.InheritSpecification

Creates a new specification for the given annotation type.

init() - Static method in class net.sf.basedb.clients.web.extensions.service.Services

Initialise and start the installed services.

init() - Method in class net.sf.basedb.clients.web.servlet.Download

init() - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet

init() - Method in class net.sf.basedb.clients.web.servlet.PlotServlet

init() - Method in class net.sf.basedb.clients.web.servlet.RssNewsFeed

init() - Static method in class net.sf.basedb.core.BatchUtil

Generate SQL for all BatchableData classes for insert, update and delete operations.

init() - Static method in class net.sf.basedb.core.Config

Loads the settings from the configuration file.

init() - Static method in class net.sf.basedb.core.ExtendedProperties

Initialize the class.

init() - Static method in class net.sf.basedb.core.Keyring

init() - Static method in class net.sf.basedb.core.Metadata

init() - Static method in class net.sf.basedb.core.PredefinedQuery

Load and parse the file with predefined queries.

init() - Static method in class net.sf.basedb.core.QueryExecutor

This will create a new thread for each query.

init() - Static method in class net.sf.basedb.core.QueryRuntimeFilterFactory

init() - Static method in class net.sf.basedb.core.RawDataTypes

Initialize the class.

init() - Static method in class net.sf.basedb.core.RawDataUtil

Initialise the class.

init() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration

init() - Static method in class net.sf.basedb.core.SystemItems

Initialize the class and load all mappings for item.systemId --> item.id and for RoleKeyData.itemType --> RoleKeyData.id

init() - Static method in class net.sf.basedb.core.Version

Loads the settings from the configuration file.

init() - Static method in class net.sf.basedb.util.EmailUtil

init() - Method in class net.sf.basedb.util.JarClassLoader.JarClassLoaderProxy

Initialize the proxy.

init(String) - Method in class net.sf.basedb.clients.jobagent.AgentSignalReceiver

Initialise the receiver.

init(String) - Method in class net.sf.basedb.clients.web.util.SimpleSignalProgressReporter

Nothing need to be initilized.

init(String) - Method in class net.sf.basedb.core.Job.JobSignalTransporter

init(String) - Method in class net.sf.basedb.core.signal.AbstractSignalReceiver

Initialise the signal receiver.

init(String) - Method in class net.sf.basedb.core.signal.AbstractSignalTransporter

Initialise the transporter.

init(String) - Method in class net.sf.basedb.core.signal.LocalSignalReceiver

Initialise the signal receiver.

init(String) - Method in interface net.sf.basedb.core.signal.SignalReceiver

Initialise the signal receiver.

init(String) - Method in interface net.sf.basedb.core.signal.SignalTransporter

Initialise the signal transporter.

init(String) - Method in class net.sf.basedb.core.signal.SocketSignalReceiver

Initialise the receiver.

init(String, String, String) - Method in class net.sf.basedb.util.uri.http.HttpConnectionManagerFactory

Initialize this factory with some information.

init(FilterConfig) - Method in class net.sf.basedb.clients.web.servlet.CacheControlFilter

init(FilterConfig) - Method in class net.sf.basedb.clients.web.servlet.CharacterEncodingFilter

init(FilterConfig) - Method in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter

init(FilterConfig) - Method in class net.sf.basedb.clients.web.servlet.ImageRemapFilter

init(ServletContext) - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Initialise the extension system.

init(ServletContext) - Static method in class net.sf.basedb.clients.web.extensions.skin.ImageRemapperUtil

Initialized at server startup.

init(Agent) - Method in class net.sf.basedb.clients.jobagent.executors.DummyJobExecutor

init(Agent) - Method in class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor

init(Agent) - Method in class net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor

init(Agent) - Method in class net.sf.basedb.clients.jobagent.handlers.AbstractCustomRequestHandler

init(Agent) - Method in interface net.sf.basedb.clients.jobagent.handlers.CustomRequestHandler

Initialize the request handler.

init(Agent) - Method in interface net.sf.basedb.clients.jobagent.JobExecutor

Initialize the job executor.

init(Agent) - Method in class net.sf.basedb.clients.jobagent.slotmanager.InternalSlotManager

init(Agent) - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager

init(Agent) - Method in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager

init(Agent) - Method in interface net.sf.basedb.clients.jobagent.slotmanager.SlotManager

Initialize the slot manager.

init(AnnotationData) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

Initialize the snapshot with information from the given annotation.

init(AnnotationSetData) - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot

Initialise the snapshot with data from the given annotation set, including values for all primary annotations and information about inherited annotations.

init(SessionControl, ParameterValues, ParameterValues) - Method in class net.sf.basedb.core.plugin.AbstractPlugin

Store copies of the session control, plugin and job configuration.

init(SessionControl, ParameterValues, ParameterValues) - Method in interface net.sf.basedb.core.plugin.Plugin

This method is called right after the plugin object has been constructed to pass the configuration and job parameters to the plugin.

init(SessionControl, ParameterValues, ParameterValues) - Method in class net.sf.basedb.plugins.gtf.GtfReporterImporter

init(SessionControl, ParameterValues, ParameterValues) - Method in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter

init(SessionControl, ParameterValues, ParameterValues, ExternalProgramExecutor) - Method in class net.sf.basedb.plugins.executor.AbstractIOSupport

init(SessionControl, ParameterValues, ParameterValues, ExternalProgramExecutor) - Method in interface net.sf.basedb.plugins.executor.IOSupport

Replaces the regular plug-in initialisation method.

init(JspCompilationContext, JspServletWrapper) - Method in class net.sf.basedb.clients.web.extensions.XJspCompiler

Initialises the compiler.

init_key() - Method in class net.sf.basedb.util.bcrypt.BCrypt

Initialise the Blowfish key schedule

init1() - Static method in class net.sf.basedb.core.HibernateUtil

First step of initialising this class.

init2() - Static method in class net.sf.basedb.core.HibernateUtil

Second step of initialising this class.

initBean(Class<? extends Action>) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory

Create the bean object.

initBeanWithReflection(Object, Element, Presets.Preset) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader

Initialise a bean using reflection.

initCollection(BasicItem, String) - Method in class net.sf.basedb.core.DbControl

Initialise a collection on an item.

initCollection(Session, BasicData, String) - Static method in class net.sf.basedb.core.HibernateUtil

Initialise a collection on a data object.

initDatabase(SchemaGenerator.Mode, ProgressReporter, String, String) - Static method in class net.sf.basedb.core.Install

Initialise the BASE database by creating all items that are required for BASE to work properly.

initDefaultAttributes() - Method in class net.sf.basedb.clients.web.taglib.CalendarButton

initDefaultAttributes() - Method in class net.sf.basedb.clients.web.taglib.StylableTag

Initialize default attributes.

initFactory(InvokationContext<? super ConnectionManagerFactory>) - Method in class net.sf.basedb.util.uri.http.HttpConnectionManagerActionFactory

initFilters() - Method in class net.sf.basedb.core.SyncFilter

initFunTab() - Method in class net.sf.basedb.util.jep.FunctionSafeJep

Overrides the regular function lookup table by replacing it with a function table that pretends that all functions has been registered, but then generates an error message if it doesn't exists.

initGuiContexts() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport

initialised - Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl

initialised - Static variable in class net.sf.basedb.clients.web.extensions.service.Services

initialised - Variable in class net.sf.basedb.util.extensions.debug.BeanActionFactory

initialised - Variable in class net.sf.basedb.util.extensions.debug.ProxyActionFactory

initialized - Static variable in class net.sf.basedb.clients.web.taglib.Page

initialized - Static variable in class net.sf.basedb.util.EmailUtil

initializeDirtynessForSomeProperties() - Method in class net.sf.basedb.core.log.EntityDetails

We must initialize "dirtyness" for collections and some other properties from the constructor.

initialTab - Variable in class net.sf.basedb.clients.web.taglib.tab.TabControl

The ID of the tab that is initially active.

initialValue(Object) - Method in class net.sf.basedb.util.ClassLocal

Subclasses may override this to initialize the object stored for that class.

initPermissions(int, int) - Method in class net.sf.basedb.core.Annotation

READ permission is granted if the logged in user has READ permission on the associated item and annotation type.

initPermissions(int, int) - Method in class net.sf.basedb.core.AnnotationSet

READ permission is granted to all users.

initPermissions(int, int) - Method in class net.sf.basedb.core.AnyToAny

Permissions are granted based on the permission on the from item.

initPermissions(int, int) - Method in class net.sf.basedb.core.ArrayDesignBlock

WRITE and DELETE permissions are always denied.

initPermissions(int, int) - Method in class net.sf.basedb.core.BasicBatcher

Initialise the logged in user's permissions for this batcher.

initPermissions(int, int) - Method in class net.sf.basedb.core.BasicChildItem

If the logged in user has read permission for the parent, read permission is granted.

initPermissions(int, int) - Method in class net.sf.basedb.core.BasicItem

Initialise the logged in user's permissions for this item.

initPermissions(int, int) - Method in class net.sf.basedb.core.BioAssay

Deny DELETE permission.

initPermissions(int, int) - Method in class net.sf.basedb.core.BioMaterialEvent

READ permission is granted and DELETE permissions is denied to evereyone for creation events.

initPermissions(int, int) - Method in class net.sf.basedb.core.BioPlateEventParticipant

initPermissions(int, int) - Method in class net.sf.basedb.core.ChangeHistory

WRITE permission and higher is always denied.

initPermissions(int, int) - Method in class net.sf.basedb.core.ChildItem

If the logged in user has read permission for the parent, read permission is granted.

initPermissions(int, int) - Method in class net.sf.basedb.core.ClientDefaultSetting

READ permission is granted if the logged in user has READ permission to the client application.

initPermissions(int, int) - Method in class net.sf.basedb.core.DataCubeColumn

Deny DELETE permission.

initPermissions(int, int) - Method in class net.sf.basedb.core.Directory

initPermissions(int, int) - Method in class net.sf.basedb.core.DiskUsage

READ permission is granted if the logged in user is the owner of this disk usage.

initPermissions(int, int) - Method in class net.sf.basedb.core.FeatureBatcher

Grant read permission if the logged in user has read permission to the array design.

initPermissions(int, int) - Method in class net.sf.basedb.core.File

Check the write protected flag and deny DELETE if it is set.

initPermissions(int, int) - Method in class net.sf.basedb.core.FileSet

READ permission is granted to all users.

initPermissions(int, int) - Method in class net.sf.basedb.core.FileSetMember

READ permission is granted to all users.

initPermissions(int, int) - Method in class net.sf.basedb.core.GlobalDefaultSetting

READ permission is always granted.

initPermissions(int, int) - Method in class net.sf.basedb.core.Group

If the logged in user is a member of this group, read permission is granted.

initPermissions(int, int) - Method in class net.sf.basedb.core.ItemKey

WRITE permission is always denied.

initPermissions(int, int) - Method in class net.sf.basedb.core.ItemSubtype

If this is a system protocol type, delete and create permissions are revoked.

initPermissions(int, int) - Method in class net.sf.basedb.core.Job

Grant read permission if the logged in user has read permission to the experiment the job belongs to.

initPermissions(int, int) - Method in class net.sf.basedb.core.Message

Read, write an delete permission is granted if the logged in user is the same as the user the message is to.

initPermissions(int, int) - Method in class net.sf.basedb.core.News

Read permission is granted if today is between the start and end date.

initPermissions(int, int) - Method in class net.sf.basedb.core.OwnedItem

If the logged in user is the owner of this item, DELETE, SET_OWNER and SET_PERMISSION permission is granted.

initPermissions(int, int) - Method in class net.sf.basedb.core.Platform

Deny deletion of the GENERIC and Affymetrix platform.

initPermissions(int, int) - Method in class net.sf.basedb.core.PluginType

All users get READ access.

initPermissions(int, int) - Method in class net.sf.basedb.core.Project

If the logged in user is a member of this project, read or use permission is granted.

initPermissions(int, int) - Method in class net.sf.basedb.core.ProjectKey

WRITE permission is always denied.

initPermissions(int, int) - Method in class net.sf.basedb.core.Quantity

If this is a system quantity, delete and create permissions are revoked.

initPermissions(int, int) - Method in class net.sf.basedb.core.Quota

The logged in user has read permission to the quota assigned to him/her, directly or through group quota.

initPermissions(int, int) - Method in class net.sf.basedb.core.QuotaType

The logged in user has read permission to the quota assigned to him/her.

initPermissions(int, int) - Method in class net.sf.basedb.core.RawDataBatcher

Grant read permission if the logged in user has read permission to the raw bioassay.

initPermissions(int, int) - Method in class net.sf.basedb.core.ReporterCloneTemplate

Locked templates are READ-able by all, and everything else is denied.

initPermissions(int, int) - Method in class net.sf.basedb.core.Role

If the logged in user is a member of this role, read permission is granted.

initPermissions(int, int) - Method in class net.sf.basedb.core.RoleKey

CREATE and DELETE permissions are always denied.

initPermissions(int, int) - Method in class net.sf.basedb.core.RootRawBioAssay

Deny DELETE permission.

initPermissions(int, int) - Method in class net.sf.basedb.core.Session

READ permission is granted if the logged in user is the owner of this session.

initPermissions(int, int) - Method in class net.sf.basedb.core.Setting

Add permissions granted to Item.SETTING.

initPermissions(int, int) - Method in class net.sf.basedb.core.SharedItem

Grant permissions according to the item and project keys.

initPermissions(int, int) - Method in class net.sf.basedb.core.User

If the logged in user is the same as this user RESTRICTED_WRITE permissions is granted, unless it is a multiuser account.

initPermissions(int, int) - Method in class net.sf.basedb.core.UserClientSetting

READ permission is granted if the logged in user is the owner of this setting.

initPermissions(int, int) - Method in class net.sf.basedb.core.UserDefaultSetting

READ permission is granted if the logged in user is the owner of this setting.

initPermissions(int, int) - Method in class net.sf.basedb.core.UserDevice

DELETE permission is granted if the logged in user is the owner of this device.

initPlatforms(Session) - Static method in class net.sf.basedb.core.RawDataTypes

Load file-only platforms and create raw data types for them.

initPropertyFilters(Map<String, PropertyFilterData>) - Method in class net.sf.basedb.core.ItemContext

Initialize the property filters by loading them from the given map.

initProxy(Class<? extends Action>) - Method in class net.sf.basedb.util.extensions.debug.ProxyActionFactory

Initialise the proxy class.

initQuery(ItemQuery<I>, String) - Method in class net.sf.basedb.util.overview.GenericOverview

Same as GenericOverview.initQuery(ItemQuery, Order...) but easier to use when sorting the items in ascending order by a single column.

initQuery(ItemQuery<I>, String) - Method in interface net.sf.basedb.util.overview.OverviewContext

Same as OverviewContext.initQuery(ItemQuery, Order...) but easier to use when sorting the items in ascending order by a single column.

initQuery(ItemQuery<I>, Order...) - Method in class net.sf.basedb.util.overview.GenericOverview

Initialise a query with "global options" and optionally a sort order.

initQuery(ItemQuery<I>, Order...) - Method in interface net.sf.basedb.util.overview.OverviewContext

Initialise a query with "global options" and optionally a sort order.

initReferenceQuery(DbControl, IdMethod, ItemQuery<T>, boolean) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Initialise a query that is used to find referenced items.

initReporterCache(DbControl) - Method in class net.sf.basedb.clients.web.ExperimentExplorer

initStaticFields(PageContext) - Static method in class net.sf.basedb.clients.web.taglib.Page

Initialize static fields.

INNER - Enum constant in enum class net.sf.basedb.core.query.JoinType

Use an inner join, ie. only select rows present in both tables.

innerJoin(String, String) - Static method in class net.sf.basedb.core.query.Hql

Same as innerJoin(null, propert, joinedAlias)

innerJoin(String, String, String) - Static method in class net.sf.basedb.core.query.Hql

Create an inner join query element.

innerJoin(String, String, String, boolean) - Static method in class net.sf.basedb.core.query.Hql

Same as innerJoin(null, propert, joinedAlias, null, false)

innerJoin(String, String, String, Restriction, boolean) - Static method in class net.sf.basedb.core.query.Hql

Create an inner join query element and optionally prefetch the joined items in the same query.

innerJoin(String, AnnotationType, String) - Static method in class net.sf.basedb.core.query.Annotations

Create an inner join between an already joined element of a query and the annotation values for the given annotation type.

innerJoin(AnnotationType, String) - Static method in class net.sf.basedb.core.query.Annotations

Create an inner join between the root element of a query and the annotation values for the given annotation type.

Input - Class in net.sf.basedb.clients.web.taglib

This tag is used to make it easier to add <input> elements on a BASE web page.

Input() - Constructor for class net.sf.basedb.clients.web.taglib.Input

InputStreamCombiner - Class in net.sf.basedb.util

An input stream implementation that reads one or more input streams sequentially.

InputStreamCombiner(InputStream...) - Constructor for class net.sf.basedb.util.InputStreamCombiner

Create a new stream combiner using the given streams to read from

InputStreamLocator - Interface in net.sf.basedb.util.bfs

Defines a generic interface for opening an input stream from a named resource.

InputStreamSplitter - Class in net.sf.basedb.util

This class can be used to split an input stream into one or more additional output streams.

InputStreamSplitter(InputStream, boolean, boolean, OutputStream...) - Constructor for class net.sf.basedb.util.InputStreamSplitter

Create a new input stream splitter.

InputStreamSplitter(InputStream, OutputStream...) - Constructor for class net.sf.basedb.util.InputStreamSplitter

Create a new input stream splitter.

InputStreamTracker - Class in net.sf.basedb.util

This class is used to keep track of the number of bytes read from the underlying input stream.

InputStreamTracker(InputStream) - Constructor for class net.sf.basedb.util.InputStreamTracker

Create a new input stream tracker.

InputStreamTracker(InputStream, InputStreamTracker.ScaleFactor) - Constructor for class net.sf.basedb.util.InputStreamTracker

Create a new input stream tracker.

InputStreamTracker.CurvedScaleFactor - Class in net.sf.basedb.util

Apply a curved scale factor that has a max upper limit.

InputStreamTracker.IdentityScaleFactor - Class in net.sf.basedb.util

Do not scale number of bytes.

InputStreamTracker.LinearScaleFactor - Class in net.sf.basedb.util

Apply a linear scale factor so that when we have read N actual bytes the getNumRead() method return N*scale bytes.

InputStreamTracker.ScaleFactor - Interface in net.sf.basedb.util

A scale factor can be used to match number of read bytes to something that better resembles actual progress.

InReporterListFunction - Class in net.sf.basedb.util.jep

A JEP function class that adds a inList(reporterListId) function to a JEP expression parser.

InReporterListFunction(DbControl) - Constructor for class net.sf.basedb.util.jep.InReporterListFunction

Create a new instance of this function.

InRestriction - Class in net.sf.basedb.core.query

Compare if one expression is contained in a set of other expressions: e1 IN (e2[0], e2[1], ...)

InRestriction(Expression, Expression...) - Constructor for class net.sf.basedb.core.query.InRestriction

insert(int, I) - Method in class net.sf.basedb.core.PositionExtraValueBatcher

Insert an extra value for a given position coordinate.

insert(int, ReporterData) - Method in class net.sf.basedb.core.PositionBatcher

Link a position to a reporter.

insert(short, int) - Method in class net.sf.basedb.core.FilterBatcher

Insert a column/position coordinate that passed the filter.

insert(short, int, float...) - Method in class net.sf.basedb.core.SpotBatcher

Insert intensities for a given column/position coordinate.

insert(short, int, I) - Method in class net.sf.basedb.core.SpotExtraValueBatcher

Insert an extra value for a given column/position coordinate.

insert(short, int, RawData) - Method in class net.sf.basedb.core.MappingBatcher

Link a spot to a raw data.

insert(D) - Method in class net.sf.basedb.core.BasicBatcher

Insert a data object.

insert(Object) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

insert(Object...) - Method in class net.sf.basedb.core.AnnotationBatcher.InsertBatcher

Execute an insert SQL statement with the given parameter values.

insert(String, Object) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

insert(AbstractSqlQuery) - Method in class net.sf.basedb.core.FilterBatcher

Insert column/position coordinates using a query.

insert(AbstractSqlQuery) - Method in class net.sf.basedb.core.MappingBatcher

Insert mapping to raw spots using a query.

insert(AbstractSqlQuery) - Method in class net.sf.basedb.core.PositionBatcher

Insert position/reporter links using a query.

insert(AbstractSqlQuery) - Method in class net.sf.basedb.core.PositionExtraValueBatcher

Insert position extra values using a query.

insert(AbstractSqlQuery) - Method in class net.sf.basedb.core.SpotBatcher

Insert spot intensities using a query.

insert(AbstractSqlQuery) - Method in class net.sf.basedb.core.SpotExtraValueBatcher

Insert extra values using a query.

insert(FeatureData) - Method in class net.sf.basedb.core.FeatureBatcher

Set the position number and add the feature to the insert queue.

insert(RawData) - Method in class net.sf.basedb.core.RawDataBatcher

insert(RawData, String, String) - Method in class net.sf.basedb.core.RawDataBatcher

Insert a raw data spot and verify the external id of the reporter.

insert(ReporterData) - Method in class net.sf.basedb.core.ReporterBatcher

Insert and add the external reporter id to the internal cache.

insertable - Variable in class net.sf.basedb.core.ExtendedProperty

InsertBatcher(Connection, String, int...) - Constructor for class net.sf.basedb.core.AnnotationBatcher.InsertBatcher

Prepare a new batcher for the given SQL statement.

insertCount - Variable in class net.sf.basedb.core.BasicBatcher

insertCountTotal - Variable in class net.sf.basedb.core.BasicBatcher

Counts the number of inserts done by the batcher.

insertIntoAnnotations - Variable in class net.sf.basedb.core.AnnotationBatcher

insertIntoAnnotationSets - Variable in class net.sf.basedb.core.AnnotationBatcher

insertIntoDetails - Variable in class net.sf.basedb.core.LogControl

insertIntoParameterValues - Variable in class net.sf.basedb.core.AnnotationBatcher

insertPropertyOrder - Variable in class net.sf.basedb.core.BasicBatcher

insertSql - Variable in class net.sf.basedb.core.BasicBatcher

insertSql - Variable in class net.sf.basedb.core.ReporterCloneBatcher

The statement that inserts cloned reporter data.

insertSqlStatement - Variable in class net.sf.basedb.core.ReporterCloneBatcher

The SQL string for the ReporterCloneBatcher.insertSql statement.

insertStatement - Variable in class net.sf.basedb.core.BasicBatcher

insertValues - Variable in class net.sf.basedb.core.AnnotationBatcher

inspectSchemaGenerationSQL(String, Dialect, SchemaGenerator.Mode) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine

Skip all "create index ..." statements.

inspectSchemaGenerationSQL(String, Dialect, SchemaGenerator.Mode) - Method in interface net.sf.basedb.core.dbengine.DbEngine

Let the DbEninge inspect a schema generation sql statment and possible modify it before it is sent to the database.

inspectWorkingDirectory() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

Check the working directory for new files.

Install - Class in net.sf.basedb.core

This class contains static methods used to install items into an empty database.

Install() - Constructor for class net.sf.basedb.core.Install

INSTALL - Enum constant in enum class net.sf.basedb.core.hibernate.SchemaGenerator.Mode

Creating a fresh installation.

Install.ItemSubtypeFT - Class in net.sf.basedb.core

Install.PlatformFT - Class in net.sf.basedb.core

installation - Variable in class net.sf.basedb.core.Application.StartupOptions

installation(boolean) - Method in class net.sf.basedb.core.Application.StartupOptions

Set to TRUE when starting a new installation.

InstalledFileProcessor - Class in net.sf.basedb.clients.web.extensions

File processor implementation that sets a final result status for each processed file (eg.

InstalledFileProcessor(ProcessResults) - Constructor for class net.sf.basedb.clients.web.extensions.InstalledFileProcessor

installedFiles - Variable in class net.sf.basedb.util.extensions.manager.Settings

InstalledFilter - Class in net.sf.basedb.util.extensions.manager.filter

Filter implementation for extension files that allow installed files to pass.

InstalledFilter(Settings) - Constructor for class net.sf.basedb.util.extensions.manager.filter.InstalledFilter

Create a new filter.

InstalledFilter(Settings, Filter<ExtensionsFile>) - Constructor for class net.sf.basedb.util.extensions.manager.filter.InstalledFilter

Create a new filter with an optional chained parent filted.

installedObjects - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsManager

installedSchemaVersion - Variable in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration

InstallFilter - Class in net.sf.basedb.clients.web.extensions

Filter implementation that selects only those extensions that was selected by the user in the gui.

InstallFilter(HttpServletRequest) - Constructor for class net.sf.basedb.clients.web.extensions.InstallFilter

InstallFilter(HttpServletRequest, boolean) - Constructor for class net.sf.basedb.clients.web.extensions.InstallFilter

Create a filter that allow us to ignore the error flag.

installHelpTexts(Client, boolean, InputStream, String) - Method in class net.sf.basedb.plugins.HelpImporter

This method installs the helptexts from an inputstream.

installMode - Variable in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration

installOrUpdate(DbControl, PluginInfo, String, ItemKey) - Static method in class net.sf.basedb.core.PluginDefinition

Install or update the plug-in definition with information from the info object.

installUnits(String, boolean) - Static method in class net.sf.basedb.core.Install

INSTANCE - Static variable in class net.sf.basedb.clients.web.extensions.login.PasswordLoginFormFactory

The default password login form.

INSTANCE - Static variable in class net.sf.basedb.util.resources.Utf8PropertiesResourceBundleControl

The one and only instance.

InstanceOfFilter<T> - Class in net.sf.basedb.util.filter

A filter implementation that accepts all objects that are (sub)classes of a specified class.

InstanceOfFilter(Class<?>, boolean) - Constructor for class net.sf.basedb.util.filter.InstanceOfFilter

Create a new filter.

instances - Static variable in class net.sf.basedb.core.Metadata

Cache of Metadata instances.

INT - Enum constant in enum class net.sf.basedb.core.Type

Integer type.

integer(int) - Static method in class net.sf.basedb.core.query.Expressions

Create a constant expression from an integer.

INTEGER - Enum constant in enum class net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType

INTEGER - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper

IntegerConverter - Class in net.sf.basedb.util.jep.convert

Convert an Integer constant to a Query API Expression.

IntegerConverter() - Constructor for class net.sf.basedb.util.jep.convert.IntegerConverter

IntegerExpression - Class in net.sf.basedb.core.query

A constant integer expression.

IntegerExpression(int) - Constructor for class net.sf.basedb.core.query.IntegerExpression

IntegerFormatter - Class in net.sf.basedb.util.formatter

Formats a number as an integer.

IntegerFormatter(boolean) - Constructor for class net.sf.basedb.util.formatter.IntegerFormatter

Create a new integer formatter.

IntegerFormatter(boolean, Character) - Constructor for class net.sf.basedb.util.formatter.IntegerFormatter

Create a new integer formatter with a thousands separator.

IntegerParameterType - Class in net.sf.basedb.core

This class represent a parameter type that is an integer.

IntegerParameterType() - Constructor for class net.sf.basedb.core.IntegerParameterType

Create a new integer parameter type, without any limits and allowing null values.

IntegerParameterType(Integer, Integer, Integer, boolean) - Constructor for class net.sf.basedb.core.IntegerParameterType

Create a new integer parameter type.

IntegerParameterType(Integer, Integer, Integer, boolean, int, int, int, List<Integer>) - Constructor for class net.sf.basedb.core.IntegerParameterType

IntegerParameterValueData - Class in net.sf.basedb.core.data

Integer parameter value.

IntegerParameterValueData() - Constructor for class net.sf.basedb.core.data.IntegerParameterValueData

IntegerParameterValueData(Integer...) - Constructor for class net.sf.basedb.core.data.IntegerParameterValueData

IntegerUtil - Class in net.sf.basedb.core

Utility methods that will make it easier to implement data validation for integer attributes.

IntegerUtil() - Constructor for class net.sf.basedb.core.IntegerUtil

IntegerWriter - Class in net.sf.basedb.core.migrate

Database-independent writer implementation that writes integer values from a result set.

IntegerWriter(ResultSet, int, Writer, char[]) - Constructor for class net.sf.basedb.core.migrate.IntegerWriter

INTENSITY - Enum constant in enum class net.sf.basedb.core.plugin.Plugin.MainType

INTENSITY_EXPRESSION - Enum constant in enum class net.sf.basedb.core.Formula.Type

The formula represents an intensity measurement expression.

INTENSITY_TRANSFORMATION - Enum constant in enum class net.sf.basedb.core.Formula.Type

The formula represents a intensity transformation expression.

IntensityCalculator - Interface in net.sf.basedb.util

This interface is used together with the IntensityCalculatorUtil class to help a plugin calculate intensities from raw data spots.

IntensityCalculatorPlugin - Class in net.sf.basedb.plugins

This plugin provides methods to calculate the intensity for a root bioassayset using different formulas.

IntensityCalculatorPlugin() - Constructor for class net.sf.basedb.plugins.IntensityCalculatorPlugin

Constructor should be empty.

IntensityCalculatorUtil - Class in net.sf.basedb.util

This is a utility class for plugins that calculate intensities from raw spot data.

IntensityCalculatorUtil() - Constructor for class net.sf.basedb.util.IntensityCalculatorUtil

IntensityCalculatorUtil.JepIntensityCalculatorImpl - Class in net.sf.basedb.util

An implementation of the IntensityCalculator interface using JEP expressions.

IntensityFormula - Class in net.sf.basedb.core

Holds information about the formulas used to calculate intensities from a raw data spot.

IntensityFormula(String, String, String, String[]) - Constructor for class net.sf.basedb.core.IntensityFormula

Create a new intensity formula.

intensityTransform - Variable in class net.sf.basedb.core.data.BioAssaySetData

IntensityTransform - Enum Class in net.sf.basedb.core

Gives information in what way spot intensities has been transformed before they were stored in the database.

IntensityTransform(int, String, boolean, Formula.AverageMethod) - Constructor for enum class net.sf.basedb.core.IntensityTransform

Creates a new intensity transform.

interactive - Variable in class net.sf.basedb.core.data.PluginDefinitionData

InteractivePlugin - Interface in net.sf.basedb.core.plugin

An interactive plugin is a Plugin that supports interactive configuration in a user session.

interfaceName - Variable in class net.sf.basedb.core.data.PluginTypeData

INTERNAL - Static variable in class net.sf.basedb.core.authentication.AuthenticationMethod

This is special-case internal login used by job queue, etc.

INTERNAL_ID - Static variable in class net.sf.basedb.plugins.batchimport.InternalIdMethod

Use the internal ID for finding items.

internalFile - Variable in class net.sf.basedb.core.File

The path to the internal file.

internalId - Variable in class net.sf.basedb.core.authentication.AuthenticatedUser

internalId - Variable in class net.sf.basedb.util.extensions.xml.PluginInfo

internalIdColumnMapping - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

internalIdColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

InternalIdMethod - Class in net.sf.basedb.plugins.batchimport

Identification method implementation that finds an item by using the getById() method.

InternalIdMethod(String, String) - Constructor for class net.sf.basedb.plugins.batchimport.InternalIdMethod

Create a new id method.

internalJobQueue - Static variable in class net.sf.basedb.core.Application

The internal job queue reference if it is enabled.

InternalJobQueue - Class in net.sf.basedb.core

A simple implementation of a job queue that executes jobs in order of priority and longest waiting time.

InternalJobQueue() - Constructor for class net.sf.basedb.core.InternalJobQueue

Create the job queue.

InternalJobQueue.JobQueueKeyring - Class in net.sf.basedb.core

Our own keyring containing the permissions we need to execute the jobs.

InternalJobQueue.JobRunner - Class in net.sf.basedb.core

Encapsulates the running of a job in a separate thread.

internalName - Variable in class net.sf.basedb.core.data.FileData

internalPrintBofMarker() - Method in class net.sf.basedb.util.bfs.MetadataWriter

Prints the beginning-of-file marker.

internalPrintComment(String) - Method in class net.sf.basedb.util.bfs.MetadataWriter

Print a single-line comment.

internalPrintSection(String) - Method in class net.sf.basedb.util.bfs.MetadataWriter

Prints a section header assuming that the name has already been encoded.

internalPrintValue(String, String) - Method in class net.sf.basedb.util.bfs.MetadataWriter

Prints a section entry assuming that the key and value has already been encoded.

InternalSlotManager - Class in net.sf.basedb.clients.jobagent.slotmanager

The internal slot manager assigns slot to jobs based on their estimated execution time.

InternalSlotManager() - Constructor for class net.sf.basedb.clients.jobagent.slotmanager.InternalSlotManager

interruptHandler - Static variable in class net.sf.basedb.core.signal.ThreadSignalHandler

Keep per-thread interupt handlers.

InterruptHandler - Interface in net.sf.basedb.core.signal

An interface for handling thread interrupts.

intersect(IdListRestriction) - Method in class net.sf.basedb.core.query.IdListRestriction

Merge this id list with another list.

intersection(Collection<ItemList>, ItemList.DelayedAdditionManager) - Static method in class net.sf.basedb.core.ItemList

Create a set with the intersection of the items in the given lists.

intersection(Collection<ReporterList>) - Static method in class net.sf.basedb.core.ReporterList

Create a set with the intersection of the reporter ID:s in the given lists.

interval - Variable in class net.sf.basedb.clients.web.extensions.service.DummyService

interval - Variable in class net.sf.basedb.util.ProgressInputStream

IntValue(Number) - Constructor for class net.sf.basedb.util.excel.ExcelValue.IntValue

INV_LN10x2 - Static variable in class net.sf.basedb.util.ma.MACalculator

INV_LN2 - Static variable in class net.sf.basedb.plugins.LowessNormalization.SpotData

INV_LN2 - Static variable in class net.sf.basedb.util.ma.MACalculator

INV_LOG10_2 - Static variable in class net.sf.basedb.util.ma.Log10MACalculator

INV_LOG2_10x2 - Static variable in class net.sf.basedb.util.ma.Log2MACalculator

invalid - Static variable in class net.sf.basedb.core.Path

A regexp checking for invalid characters.

INVALID_CHARACTERS - Static variable in class net.sf.basedb.core.Path

These characters are not valid within a file or directory name: "~\\/:;*?<>|\""

INVALID_USE_OF_NULL_ERROR - Static variable in class net.sf.basedb.plugins.util.Parameters

The name of the parameter created by Parameters.invalidUseOfNullError(String, String, String, String...).

InvalidAndModifiedFilter - Class in net.sf.basedb.util.extensions.manager.filter

Filter implementation for extension files that allow modified but invalid files to pass.

InvalidAndModifiedFilter() - Constructor for class net.sf.basedb.util.extensions.manager.filter.InvalidAndModifiedFilter

Create a new filter.

InvalidAnnotationException - Exception in net.sf.basedb.core

InvalidAnnotationException() - Constructor for exception net.sf.basedb.core.InvalidAnnotationException

Create a new InvalidAnnotationException object.

InvalidAnnotationException(String) - Constructor for exception net.sf.basedb.core.InvalidAnnotationException

Create a new InvalidAnnotationException object with the specified message.

InvalidAnnotationException(AnnotationType, Item) - Constructor for exception net.sf.basedb.core.InvalidAnnotationException

Create a new InvalidAnnotationException object when the annotation type cannot be used for the specified item type.

invalidColumnsErrorParameter - Static variable in class net.sf.basedb.plugins.IlluminaRawDataImporter

InvalidDataException - Exception in net.sf.basedb.core

Exceptions of this type are thrown when invalid data is encountered.

InvalidDataException() - Constructor for exception net.sf.basedb.core.InvalidDataException

Create a new InvalidDataException object.

InvalidDataException(String) - Constructor for exception net.sf.basedb.core.InvalidDataException

Create a new InvalidDataException object with the specified message.

InvalidDataException(String, Throwable) - Constructor for exception net.sf.basedb.core.InvalidDataException

Create a new InvalidDataException object with the specified message.

InvalidDataException(Throwable) - Constructor for exception net.sf.basedb.core.InvalidDataException

Create a new InvalidDataException object.

invalidEnumErrorParameter - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

InvalidPasswordException - Exception in net.sf.basedb.core.authentication

This exception can be thrown when the password is invalid.

InvalidPasswordException - Exception in net.sf.basedb.core

Exceptions of this type are thrown when user tries to log in, but the password is incorrect.

InvalidPasswordException(String) - Constructor for exception net.sf.basedb.core.authentication.InvalidPasswordException

Create a new InvalidPasswordException object

InvalidPasswordException(String) - Constructor for exception net.sf.basedb.core.InvalidPasswordException

Create a new InvalidPasswordException object with the specified message

InvalidPasswordException(String, String) - Constructor for exception net.sf.basedb.core.authentication.InvalidPasswordException

Create a new InvalidPasswordException object

InvalidPasswordException(String, Throwable) - Constructor for exception net.sf.basedb.core.InvalidPasswordException

Create a new InvalidPasswordException object with the specified message

InvalidPathException - Exception in net.sf.basedb.core

This exception is thrown when BASE is trying to parse a path which is invalid.

InvalidPathException(String) - Constructor for exception net.sf.basedb.core.InvalidPathException

Create a new InvalidPathException object.

InvalidRelationException - Exception in net.sf.basedb.core

Exceptions of this type are thrown when a ValidationAction has detected that a file related to the main file is invalid.

InvalidRelationException() - Constructor for exception net.sf.basedb.core.InvalidRelationException

Create a new InvalidRelationException object.

InvalidRelationException(String) - Constructor for exception net.sf.basedb.core.InvalidRelationException

Create a new InvalidRelationException object with the specified message.

InvalidRelationException(String, Throwable) - Constructor for exception net.sf.basedb.core.InvalidRelationException

Create a new InvalidRelationException object with the specified message.

InvalidRelationException(Throwable) - Constructor for exception net.sf.basedb.core.InvalidRelationException

Create a new InvalidRelationException object.

invalidUseOfNullError(String, String, String, String...) - Static method in class net.sf.basedb.plugins.util.Parameters

Create the parameter for handling required but missing values.

invalidUseOfNullErrorParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter

InvalidUseOfNullException - Exception in net.sf.basedb.core

This exception is thrown when an object field or a parameter that mustn't be null is set to null.

InvalidUseOfNullException() - Constructor for exception net.sf.basedb.core.InvalidUseOfNullException

Create a new InvalidUseOfNullException object.

InvalidUseOfNullException(String) - Constructor for exception net.sf.basedb.core.InvalidUseOfNullException

Create a new InvalidUseOfNullException object.

invariantEquals(List<?>, List<?>) - Static method in class net.sf.basedb.util.EqualsHelper

Checks if two lists contains equal elements disregarding their positions in the array.

invariantEquals(T[], T[]) - Static method in class net.sf.basedb.util.EqualsHelper

Checks if two arrays contains equal elements disregarding their positions in the array.

InverseFilter<T> - Class in net.sf.basedb.util.filter

A filter implementation that negates the result of a parent filter.

InverseFilter(Filter<? super T>) - Constructor for class net.sf.basedb.util.filter.InverseFilter

INVLN2 - Static variable in class net.sf.basedb.util.ColorGenerator

Constant holding the value of 1 / ln(2).

InvokationContext<A extends Action> - Class in net.sf.basedb.util.extensions

Keeps contextual information about a single invokation of extensions.

InvokationContext() - Constructor for class net.sf.basedb.util.extensions.InvokationContext

invoke() - Method in class net.sf.basedb.core.PluginConfigurationRequest

invoke() - Method in class net.sf.basedb.core.PluginExecutionRequest

invoke() - Method in class net.sf.basedb.core.PluginRequest

Invoke the plugin and let it do it's work.

invoke(Object, Method, Object[]) - Method in class net.sf.basedb.util.extensions.debug.ProxyActionFactory

IOSupport - Interface in net.sf.basedb.plugins.executor

This interface is a tagging interface that should be implemented by export and import plug-ins that knows how to cooperate with the external program executor.

ip - Variable in class net.sf.basedb.core.signal.SocketSignalReceiver

IS_COMPACT - Static variable in class net.sf.basedb.clients.web.ModeInfo

isAcceptableParent(Annotatable) - Method in class net.sf.basedb.util.annotations.InheritSpecification

Checks if the parent item has a subtype matching the subtype (if any) in this specification.

isAcceptedByValidator(ValidationAction) - Method in class net.sf.basedb.util.fileset.ValidatingFileSetMember

Check if the member is accepted by the given validator.

isAffymetrix(FileStoreEnabled) - Static method in class net.sf.basedb.util.affymetrix.AffymetrixUtil

Check if the item is using the affymetrix platform.

isAllowedControl(InetAddress, String) - Method in class net.sf.basedb.clients.jobagent.Agent

Check if the computer specified by the given address is allowed to control this job agent.

isAllowedHost(InetAddress) - Method in class net.sf.basedb.core.signal.SocketSignalReceiver

Checks if the specified remote host is allowed to send signals to this receiver.

isAllowedImmediateExecution() - Method in class net.sf.basedb.core.plugin.NamespaceRequestWrapper

isAllowedImmediateExecution() - Method in interface net.sf.basedb.core.plugin.Request

If this plugin has been allowed immediate execution or not.

isAllowedImmediateExecution() - Method in class net.sf.basedb.core.PluginRequest.RequestImpl

isAllowedImmediateExecution() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper

isAllowedToUseClient(String) - Method in class net.sf.basedb.core.SessionControl

Checks if this session control can be used by the given client application.

isAnExcelFile(InputStream) - Static method in class net.sf.basedb.util.excel.XlsxToCsvUtil

Check if the given stream is an Excel file by looking at the first few bytes.

isAnnotatable() - Method in enum class net.sf.basedb.core.Item

Is this an item that supports annotations?

isAnnotated() - Method in interface net.sf.basedb.core.Annotatable

Check if this item has an annotation set.

isAnnotated() - Method in class net.sf.basedb.core.AnnotatedItem

isAnnotated() - Method in class net.sf.basedb.core.BioAssay

isAnnotated() - Method in class net.sf.basedb.core.BioAssaySet

isAnnotated() - Method in class net.sf.basedb.core.PluginDefinition

isAnnotated() - Method in class net.sf.basedb.core.Project

isAnnotated() - Method in class net.sf.basedb.core.RootRawBioAssay

isAnnotated() - Method in class net.sf.basedb.core.Well

isAnnotation - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef

If the property is an annotation or not.

isAnnotation() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

isAnnotation() - Method in class net.sf.basedb.util.export.spotdata.AnnotationAssayField

isAnnotation() - Method in interface net.sf.basedb.util.export.spotdata.AssayField

A boolean flag indicating if the field is an annotation or not.

isAnnotation() - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField

isAnnotationFix() - Method in class net.sf.basedb.util.overview.Fix

If this fix involves editing an annotation or not.

isAssignable(Class<?>[], Object[]) - Static method in class net.sf.basedb.util.ClassUtil

Check if one array of class objects is assignment compatible with values in another array.

isAssociatedDataFileType(DataFileType) - Method in class net.sf.basedb.core.ItemSubtype

Checks if the given data file type is associated with this subtype or not.

isAttached(BasicItem) - Method in class net.sf.basedb.core.DbControl

Check if an item is attached to this DbControl.

isAutoLoadingChildren() - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory

Get the auto load children setting.

isAutoReload() - Method in class net.sf.basedb.util.units.UnitCache

If units that are no longer connected to a DbControl should automatcally by reloaded with the current DbControl or not.

isAveragable() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn

isAveragable() - Method in class net.sf.basedb.core.ExtendedProperty

If it makes sense to take the average of multiple values for this property or not.

isAvoiding() - Method in class net.sf.basedb.util.listable.TransformContext

isBasicItem() - Method in enum class net.sf.basedb.core.Item

Is this item representing a BasicItem object or not?

isBound(Parameter<?>) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

isCacheable() - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

isCachingResult() - Method in class net.sf.basedb.core.AbstractHqlQuery

isCachingResult() - Method in interface net.sf.basedb.core.query.HqlQuery

If the query results are cached or not.

isCallable() - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

isChange() - Method in class net.sf.basedb.clients.web.SubContext

Is the context changed or not?

isChecked() - Method in class net.sf.basedb.clients.web.taglib.Input

isChildrenLoaded() - Method in class net.sf.basedb.util.overview.Node

isClosed - Variable in class net.sf.basedb.clients.jobagent.handlers.MultiProtocolRequestHandler

isClosed - Variable in class net.sf.basedb.core.DbControl

Is the connection closed or not?

isClosed - Variable in class net.sf.basedb.core.DynamicResultIterator

isClosed - Variable in class net.sf.basedb.core.ScrollIterator

isClosed - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile

isClosed() - Method in class net.sf.basedb.clients.jobagent.handlers.MultiProtocolRequestHandler

If the request handler is closed, it will igore all method calls.

isClosed() - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator

isClosed() - Method in class net.sf.basedb.core.AbstractBatcher

Check if this batcher is closed or not.

isClosed() - Method in interface net.sf.basedb.core.Batcher

Check if the batcher has been closed or not.

isClosed() - Method in class net.sf.basedb.core.DataResultIterator

isClosed() - Method in class net.sf.basedb.core.DbControl

Check if the connection to the database has been closed.

isClosed() - Method in class net.sf.basedb.core.DynamicResultIterator

isClosed() - Method in class net.sf.basedb.core.ItemResultIterator

isClosed() - Method in interface net.sf.basedb.core.query.ResultIterator

Check if the iterator has been closed.

isClosed() - Method in class net.sf.basedb.core.ReporterScoreResultIterator

isClosed() - Method in class net.sf.basedb.core.ScrollIterator

Check if the results has been closed.

isClosed() - Method in class net.sf.basedb.core.SessionControl

If this session control has been closed or not.

isCollecting() - Method in class net.sf.basedb.util.listable.TransformContext

isColumnSticky(String) - Method in class net.sf.basedb.clients.web.taglib.table.Table

isColumnVisible(String) - Method in class net.sf.basedb.clients.web.taglib.table.Table

isCompact - Variable in class net.sf.basedb.clients.web.ModeInfo

isCompact() - Method in class net.sf.basedb.clients.web.ModeInfo

isCompressed() - Method in class net.sf.basedb.core.data.FileData

If the file is stored in a compressed format or not.

isCompressed() - Method in class net.sf.basedb.core.File

If this file is stored in a compressed format or not.

isConnected() - Method in class net.sf.basedb.core.DbControl

Deprecated.

In 3.11. Applications should use separate DbControl instead.

isConnected() - Method in class net.sf.basedb.core.hibernate.SessionWrapper

isConnected() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

isCopyingToStdout() - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog

Are log entries copied to standard output?

isCorrectBasicData(Object) - Method in class net.sf.basedb.core.plugin.GuiContext

Checks if the specified object is an instance of the BasicData subclass used by the Item in this context.

isCorrectBasicItem(Object) - Method in class net.sf.basedb.core.plugin.GuiContext

Checks if the specified object is an instance of the BasicItem subclass used by the Item in this context.

isCorrectType(Object) - Method in enum class net.sf.basedb.core.Type

Check if the value is an object of the correct type.

isCounting - Variable in class net.sf.basedb.core.AbstractQuery

If the Query.count(DbControl) method is executing or not.

isCounting() - Method in class net.sf.basedb.core.AbstractQuery

isCounting() - Method in interface net.sf.basedb.core.query.Query

Check if the query is executing the Query.count(DbControl) method or not

isDataFileFix() - Method in class net.sf.basedb.util.overview.Fix

isDebug - Static variable in class net.sf.basedb.core.Trashcan

isDebugEnabled - Variable in class net.sf.basedb.core.AnnotationBatcher

isDebugEnabled - Static variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager

isDebugEnabled - Variable in class net.sf.basedb.util.extensions.logging.ExtensionsLog

isDebugEnabled() - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog

Is the debug-level enabled?

isDebugEnabled() - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLogger

Check if DEBUG logging has been enabled or not.

isDefault - Variable in class net.sf.basedb.core.data.GroupData

isDefault - Variable in class net.sf.basedb.core.data.RoleData

isDefault() - Method in class net.sf.basedb.core.data.GroupData

If this group should be assigned to new users by default or not.

isDefault() - Method in class net.sf.basedb.core.data.RoleData

If this role should be assigned to new users by default or not.

isDefault() - Method in class net.sf.basedb.core.Group

If this group should be assigned to new users by default or not.

isDefault() - Method in class net.sf.basedb.core.Role

If this role should be assigned to new users by default or not.

isDefaultItem(BasicItem) - Method in class net.sf.basedb.core.Project

Check if the given item is a default item in this project.

isDefaultReadOnly() - Method in class net.sf.basedb.core.hibernate.SessionWrapper

isDenied() - Method in class net.sf.basedb.clients.web.taglib.Select

isDenied(int) - Method in class net.sf.basedb.core.Keyring

Checks if the DENIED bit is set in the permission.

isDenied(Permission, Item) - Method in class net.sf.basedb.core.SessionControl

Check if the logged in user has been denied the specified permission for items of the specified type.

isDeniedPermission(int, Permission) - Static method in enum class net.sf.basedb.core.Permission

Checks if the given Permission is denied by the permissions code.

isDestroyed() - Method in class net.sf.basedb.core.ArraySlide

Check if the slide is flagged as destroyed or not.

isDestroyed() - Method in class net.sf.basedb.core.BioPlate

Check if the plate has been destroyed.

isDestroyed() - Method in class net.sf.basedb.core.data.ArraySlideData

Check if the slide is flagged as destroyed or not.

isDestroyed() - Method in class net.sf.basedb.core.data.BioPlateData

If the plate has been destroyed.

isDestroyed() - Method in class net.sf.basedb.core.data.PlateData

If the plate has been destroyed.

isDestroyed() - Method in class net.sf.basedb.core.Plate

Check if the plate has been destroyed.

isDetached() - Method in class net.sf.basedb.core.BasicItem

Check if this item is attached to a DbControl object or not.

isDirty() - Method in class net.sf.basedb.core.hibernate.SessionWrapper

isDisabled() - Method in class net.sf.basedb.clients.web.taglib.Button

isDisabled() - Method in class net.sf.basedb.clients.web.taglib.Select

isDisabled() - Method in class net.sf.basedb.clients.web.taglib.table.Button

isDisabled() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData

If set, the filter is disabled and should not be used when syncing.

isDisabled() - Method in class net.sf.basedb.core.data.PluginConfigurationData

If the plugin is enabled or disabled. // Mapped in hibernate-properties-PluginConfigurationData.xml since annotation doesn't support a default value

isDisabled() - Method in class net.sf.basedb.core.data.PluginDefinitionData

If the plugin is enabled or disabled. // Mapped in hibernate-properties-PluginDefinitionData.xml since annotation doesn't support a default value

isDisabled() - Method in class net.sf.basedb.core.data.UserData

Check if this account is disabled or enabled.

isDisabled() - Method in class net.sf.basedb.core.PluginConfiguration

Checks if this plugin configuration is disabled or not.

isDisabled() - Method in class net.sf.basedb.core.PluginDefinition

Checks if this plugin is disabled or not.

isDisabled() - Method in class net.sf.basedb.core.SyncFilter

If set, this filter is disabled and is not used when syncing.

isDisabled() - Method in class net.sf.basedb.core.User

Check if this account has been disabled.

isDisabled() - Method in class net.sf.basedb.util.extensions.xml.PluginInfo

Is this plug-in enabled or not?

isDisabled() - Method in class net.sf.basedb.util.overview.validator.BasicItemNodeValidatorFactory

isDisabled() - Method in interface net.sf.basedb.util.overview.validator.NodeValidatorFactory

Check if node validation has been disabled.

isDisabled() - Method in class net.sf.basedb.util.StaticCache

Check if the cache has been disabled.

isDistinct() - Method in class net.sf.basedb.core.AbstractQuery

isDistinct() - Method in interface net.sf.basedb.core.query.Query

If this query returns distinct results of not.

isDoublingBackAllowed() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

Enabled on a multi-hop path if the path down to the related child from the parent item is allowed to traverse the same items as the path up from the source child item to the parent.

isDownloadable() - Method in enum class net.sf.basedb.core.Location

A flag indicating if a file that is stored at this location can be downloaded by a call to File.getDownloadStream(long) or File.download(java.io.OutputStream, long).

isDryRun() - Method in class net.sf.basedb.core.data.JobData

If the job should be/was executed as a dry-run job.

isDryRun() - Method in class net.sf.basedb.core.Job

Check if the job should be/was executed as a dry-run job.

isDryRun() - Method in class net.sf.basedb.core.PluginResponse

Check if the job should be executed or was executed in dry-run mode.

isEffectivelyTrusted() - Method in class net.sf.basedb.core.JobAgentSettings

If the plugin is a trusted plugin or not.

isEmpty() - Method in class net.sf.basedb.core.BioWell

Is this well empty?

isEmpty() - Method in class net.sf.basedb.core.ItemResultList

isEmpty() - Method in class net.sf.basedb.util.formatter.LookupFormatter

Checks if the lookup map is empty or not.

isEmpty() - Method in class net.sf.basedb.util.Tree

isEmptyDatabase() - Static method in class net.sf.basedb.core.HibernateUtil

Check if the main database has any tables.

isEnabled() - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

isEnabled() - Method in interface net.sf.basedb.clients.web.extensions.menu.MenuItemAction

If the menu item should be enabled or disabled.

isEnabled() - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean

isEnabled() - Method in interface net.sf.basedb.clients.web.extensions.toolbar.ButtonAction

If the button should be enabled or disabled.

isEnabled() - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean

isEnabled() - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory

isEnabled() - Static method in class net.sf.basedb.clients.web.servlet.RssNewsFeed

Check if the rss servlet has been enabled or not.

isEnabled() - Method in class net.sf.basedb.clients.web.taglib.Icon

isEnabled() - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem

isEnabled() - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu

isEnabled() - Method in class net.sf.basedb.clients.web.taglib.path.PathElement

isEnabled() - Method in class net.sf.basedb.clients.web.taglib.table.Button.ButtonActionWrapper

isEnabled() - Static method in class net.sf.basedb.util.EmailUtil

Check if email sending has been enabled for the server or not.

isEnabled(User) - Static method in class net.sf.basedb.util.EmailUtil

Check if email sending is enabled for the given user.

isEnabled(Extension<?>) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Check if an extension is enabled of disabled.

isEnabled(Extension<?>) - Method in class net.sf.basedb.util.extensions.DefaultFilter

isEnabled(Extension<?>) - Method in interface net.sf.basedb.util.extensions.ExtensionsFilter

Check if an extension is enabled or disabled.

isEnabled(Extension<?>) - Method in class net.sf.basedb.util.extensions.manager.Settings

isEnabled(Extension<?>) - Method in class net.sf.basedb.util.extensions.SingleExtensionFilter

isEnabled(ExtensionPoint<?>) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Check if an extension point is enabled of disabled.

isEnabled(ExtensionPoint<?>) - Method in class net.sf.basedb.util.extensions.DefaultFilter

isEnabled(ExtensionPoint<?>) - Method in interface net.sf.basedb.util.extensions.ExtensionsFilter

Check if an extension point is enabled or disabled.

isEnabled(ExtensionPoint<?>) - Method in class net.sf.basedb.util.extensions.manager.Settings

isEnabled(ExtensionPoint<?>) - Method in class net.sf.basedb.util.extensions.SingleExtensionFilter

isEnabledForItem(Item) - Method in class net.sf.basedb.core.AnnotationType

Check if this annotation type can be used to annotate item of the specified type.

isEnumeration - Variable in class net.sf.basedb.core.data.AnnotationTypeData

isEnumeration() - Method in class net.sf.basedb.core.AnnotationType

Check if this annotation type provides a list of predefined allowed values.

isEnumeration() - Method in class net.sf.basedb.core.data.AnnotationTypeData

If this annotation type defines a list of allowed values or not.

isEnumeration() - Method in class net.sf.basedb.core.ParameterType

Check if the parameter type enumerates the allowed values or not.

isEqualOrNull(Object, Object) - Static method in class net.sf.basedb.util.Diff3

Check if two objects are both null or equal as defined by the Object.equals(Object) method.

isEqualOrNull(String, String) - Static method in class net.sf.basedb.core.StringUtil

Check if two strings are equal or both are null.

isEqualOrNull(String, String, boolean) - Static method in class net.sf.basedb.core.StringUtil

Check if two strings are equal or both are null.

isError() - Method in class net.sf.basedb.util.ContextUtil.ContextResult

If this is an error-level object.

isExecutable() - Method in enum class net.sf.basedb.core.Job.Status

If the Job.execute(ProgressReporter, String) method can be called when the job is in this status or not.

isExecuting - Variable in class net.sf.basedb.util.timer.ThreadTimerTask

isExportable() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

isExportable() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction

A flag to indicate if it is possible to export this column with the generic table exporter or not.

isExportable() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

isExpressionOperator() - Method in enum class net.sf.basedb.core.Operator

isExtendable(String) - Static method in class net.sf.basedb.core.ExtendedProperties

Check if extended properties has been defined for the specified class.

isExtendedProperty - Variable in class net.sf.basedb.core.ClonableProperty

isExtendedProperty() - Method in class net.sf.basedb.core.ClonableProperty

Is this cloned property an extended property or a "static" property?

isExtendedProperty() - Method in class net.sf.basedb.core.data.ReporterClonePropertyData

If the column is an extended or "static" property.

isExtensionFilter(String) - Method in class net.sf.basedb.core.PropertyFilter

Checks if this filter is an extension filter.

isFailSafe() - Method in class net.sf.basedb.core.AbstractQuery

isFailSafe() - Method in interface net.sf.basedb.core.query.Query

Check if a failure of this query should still allow the current transaction to continue.

isFetchProfileEnabled(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

isFileOnly() - Method in class net.sf.basedb.core.data.PlatformData

If this platform can only be used with files.

isFileOnly() - Method in class net.sf.basedb.core.data.PlatformVariantData

If this platform variant can only be used with files.

isFileOnly() - Method in class net.sf.basedb.core.Platform

Check if the platform is a file-only platform or if it allows data to be imported into the database.

isFileOnly() - Method in class net.sf.basedb.core.PlatformVariant

Check if the platform variant is a file-only variant or if it allows data to be imported into the database.

isFileOnlyPlatform() - Method in class net.sf.basedb.core.ArrayDesign

Check if this array design uses a file-only platform or variant.

isFileOnlyPlatform() - Method in class net.sf.basedb.core.RawBioAssay

Check if this raw bioassay uses a file-only platform or variant.

isFilterable() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

isFilterable() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction

A flag to indicate if filtering on this column is enabled or not.

isFilterable() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

isFirstChild(E) - Method in class net.sf.basedb.util.Tree.Entry

Check if the specified object is the first child to this node.

isFriendOf(User) - Method in class net.sf.basedb.core.SessionControl

Check if the logged in user is a friend of of the specified user.

isFromInherited() - Method in class net.sf.basedb.util.overview.Fix

If this fix involves editing an inherited annotation or a primary annotation.

isFunction() - Method in class net.sf.basedb.util.jep.convert.AbsConverter

isFunction() - Method in class net.sf.basedb.util.jep.convert.AbstractJepConversionFunction

isFunction() - Method in class net.sf.basedb.util.jep.convert.ExpConverter

isFunction() - Method in class net.sf.basedb.util.jep.convert.IfConverter

isFunction() - Method in interface net.sf.basedb.util.jep.convert.JepConversionFunction

If this converter is a built-in function.

isFunction() - Method in class net.sf.basedb.util.jep.convert.LogarithmConverter

isFunction() - Method in class net.sf.basedb.util.jep.convert.NaturalLogarithmConverter

isFunction() - Method in class net.sf.basedb.util.jep.convert.SquareRootConverter

isHidden - Variable in class net.sf.basedb.clients.web.taglib.table.Cell

isHidden() - Method in class net.sf.basedb.core.ExtendedProperty

Check if the value of this property is hidden or not.

isHidden() - Method in class net.sf.basedb.core.PluginParameter

Check if the parameter is a hidden parameter or not.

isHomeDirectory() - Method in class net.sf.basedb.core.Directory

Returns TRUE if this directory is a subdirectory to Directory.HOME.

isIdentifier - Variable in class net.sf.basedb.core.data.AnnotationTypeData

isIdentifier() - Method in class net.sf.basedb.core.AnnotationType

If this flag is set, annotation values are considered to be alternate identifiers for the items they belong to.

isIdentifier() - Method in class net.sf.basedb.core.data.AnnotationTypeData

If this flag is set, annotation values can be used as identifiers to items.

isIdentifierColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

Column mapping parameter for "Is identifier" flag.

isIdentifierMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

isIgnored() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile

Is this an extension file that should be ignored?

isIgnoredFile(File) - Method in class net.sf.basedb.util.extensions.manager.Settings

Check if the given file is marked as ignored.

isIgnoringActiveProject() - Method in class net.sf.basedb.core.Annotation

Checks if this annotation is ignoring the currently active project.

isImpersonated() - Method in class net.sf.basedb.core.SessionControl

Check if the logged in user was impersonated by another user.

isImportable(InputStream) - Method in interface net.sf.basedb.core.plugin.AutoDetectingImporter

Check if the given InputStream can be imported by this plugin.

isImportable(InputStream) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

isImportable(InputStream) - Method in class net.sf.basedb.plugins.CdfFileReporterImporter

isImportable(InputStream) - Method in class net.sf.basedb.plugins.HelpImporter

isImportable(InputStream) - Method in class net.sf.basedb.plugins.PluginConfigurationImporter

isImportable(FlatFileParser) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

This method is called by the AbstractFlatFileImporter.isImportable(InputStream) method after FlatFileParser.nextSection() and FlatFileParser.parseHeaders() has been called and if data has been found.

isImportable(FlatFileParser) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter

Check that the first line contains the text "Illumina"

isImportable(FlatFileParser) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter

Check that the file is a TAM or MwBr file.

IsImportableFilter(File, Filter<? super ContextUtil.ContextResult>) - Constructor for class net.sf.basedb.util.AutoDetectFileFormat.IsImportableFilter

isInactive() - Method in class net.sf.basedb.core.data.KitData

A flag indicating if this kit is no longer active.

isInactive() - Method in class net.sf.basedb.core.Kit

Check if the kit is inactive.

isInCategory(AnnotationType) - Method in class net.sf.basedb.core.AnnotationTypeCategory

Checks if the given annotation type is a member in this category.

isInCategoryOrSubtype(AnnotationTypeCategory, ItemSubtype) - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil

Checks if this annotation type is related to the given category or subtype.

isIncluded(Collection<Include>) - Method in class net.sf.basedb.core.AbstractEntityQuery

isIncluded(Collection<Include>) - Method in interface net.sf.basedb.core.query.EntityQuery

isIncluded(Include...) - Method in class net.sf.basedb.core.AbstractEntityQuery

isIncluded(Include...) - Method in interface net.sf.basedb.core.query.EntityQuery

Check which options are set for the items to include in the result

isInContext() - Method in class net.sf.basedb.util.ContextUtil.ContextResult

If the context check was successful and generate no warnings or error.

isInContext(GuiContext) - Method in class net.sf.basedb.core.PluginDefinition

Check if it makes sense to use this plugin in the context of the specified item.

isInContext(GuiContext, Object) - Method in class net.sf.basedb.clients.web.plugins.SimpleExport

isInContext(GuiContext, Object) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

Check that the item is a bioassayset/derived bioassay and that the logged in user has permission to use the current item.

isInContext(GuiContext, Object) - Method in interface net.sf.basedb.core.plugin.InteractivePlugin

Check if the plugin can be used on the specified object.

isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter

isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.Base1PluginExecuter

Checks if the BioAssaySet has the number of channels specified by the configuration and that it has the extra values.

isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin

isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.BfsExporterPlugin

isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.CdfFileReporterImporter

If used from an array design context, verify that the array design is an affymetrix chip.

isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.executor.AbstractIOSupport

isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.FormulaFilter

isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.GalExporter

isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter

isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.HelpExporter

isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.HelpImporter

isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter

If used from an experiment context, verify that the experiment is an 'illumina' experiment and that the logged in user has permission to write.

isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin

Check that the current experiment stores it's raw data in the database.

isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.JepExtraValueCalculator

isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.JepIntensityTransformer

isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.LowessNormalization

isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator

Adds check of the item subtype.

isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.MedianRatioNormalization

isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.PackedFileExporter

Check that at least one file or directory has been selected.

isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.PlateFlatFileImporter

Always null, since plugin doesn't operate on individual items.

isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.PlateMappingExporter

Always null.

isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.PlateMappingImporter

Always null.

isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.PluginConfigurationExporter

isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.PluginConfigurationImporter

isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter

Returns null if the item is a ArrayDesign that doesn't already have any features and isn't an affy design.

isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter

Returns null if the item is a RawBioAssay of the correct RawDataType and doesn't already have spots.

isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter

Null if the context is Item.REPORTERLIST and the item is a ReporterList.

isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

Returns null if the item is a ArrayDesign that doesn't already have any features and is using a supported platform/variant.

isInContext(GuiContext, Object) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker

IsInContextFilter() - Constructor for class net.sf.basedb.util.ContextUtil.IsInContextFilter

isInDatabase() - Method in class net.sf.basedb.core.BasicItem

Checks if the item has been saved to the database or not.

isIndexed() - Method in class net.sf.basedb.core.VirtualColumn

If the column is indexed or not.

isInherited(Annotation) - Method in class net.sf.basedb.core.AnnotationSet

Check if an annotation is inherited or not by this annotation set.

isInInsertQueue(String) - Method in class net.sf.basedb.core.ReporterBatcher

isInitialised - Static variable in class net.sf.basedb.core.BatchUtil

isInitialised - Static variable in class net.sf.basedb.core.Config

isInitialised - Static variable in class net.sf.basedb.core.ExtendedProperties

isInitialised - Static variable in class net.sf.basedb.core.HibernateUtil

isInitialised - Static variable in class net.sf.basedb.core.Keyring

isInitialised - Static variable in class net.sf.basedb.core.Metadata

isInitialised - Static variable in class net.sf.basedb.core.PredefinedQuery

isInitialised - Static variable in class net.sf.basedb.core.QueryRuntimeFilterFactory

isInitialised - Static variable in class net.sf.basedb.core.RawDataTypes

isInitialised - Static variable in class net.sf.basedb.core.RawDataUtil

isInitialised - Static variable in class net.sf.basedb.core.SystemItems

isInitialized - Variable in class net.sf.basedb.util.JarClassLoader.JarClassLoaderProxy

isInitialized() - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Is the extension system initialized?

isInRelatedCategory(AnnotationType) - Method in class net.sf.basedb.core.ItemSubtype

Checks if the given annotation type is a member in any category that is related to this subtype.

isInsertable() - Method in class net.sf.basedb.core.ExtendedProperty

Check if the value of this property should be inserted into the datbase when creating new items.

isInstalled() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile

Is this file installed into the system or not?

isInstalled() - Method in class net.sf.basedb.util.extensions.xml.PluginInfo

Is this plug-in installed or not?

isInstalledFile(File) - Method in class net.sf.basedb.util.extensions.manager.Settings

Check if the given file is marked as installed.

isInSync(DbControl) - Method in class net.sf.basedb.core.ItemList

Checks if all enabled sync filters appears to be in sync or not.

isInSync(DbControl) - Method in class net.sf.basedb.core.SyncFilter

Checks if the items that are currently matching this filter are the same as the items that matched it during the last sync.

isInteractive() - Method in class net.sf.basedb.core.data.PluginDefinitionData

If the plugin is interactive or not.

isInteractive() - Method in class net.sf.basedb.core.PluginDefinition

Check if the plugin is interactive or not.

isInWell() - Method in class net.sf.basedb.core.MeasuredBioMaterial

Check if this biomaterial is located in a well on a bioplate or not.

isJar - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile

isJar() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile

If the file name ends with '.jar' the file is considered a JAR file.

isJoinedToTransaction() - Method in class net.sf.basedb.core.hibernate.SessionWrapper

isLastChild(E) - Method in class net.sf.basedb.util.Tree.Entry

Check if the specified object is the last child to this node.

isLazy() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn

Is this column lazy-loaded?

isListening() - Method in class net.sf.basedb.util.jobagent.JobAgentServerConnection

Is a listener active or not for this server.

isListOperator - Variable in enum class net.sf.basedb.core.Operator

isListOperator() - Method in enum class net.sf.basedb.core.Operator

Gets if the operator should be used with a list or not.

isLocalHost(InetAddress) - Static method in class net.sf.basedb.util.SocketUtil

Check if the specfied address is the local host or not.

isLocked() - Method in class net.sf.basedb.clients.web.taglib.table.Navigator

isLocked() - Method in class net.sf.basedb.core.data.ReporterCloneTemplateData

The template is locked when it is used by a VirtualDbData.

isLocked() - Method in class net.sf.basedb.core.ReporterCloneTemplate

If the template is locked it means that it is used by an experiment and can't be modified or deleted.

isLocked() - Method in class net.sf.basedb.util.Enumeration

isLockedColumns() - Method in class net.sf.basedb.util.bfs.DataWriter

Checks if the number of columns has been locked or not.

isLockedInWell() - Method in class net.sf.basedb.core.MeasuredBioMaterial

Check if this biomaterial is placed in a well that it can't be removed from.

isLogarithmic() - Method in class net.sf.basedb.core.Coloring

If we should take the logarithm of values before the color is generated or not.

isLogarithmic() - Method in class net.sf.basedb.core.data.ColoringData

If values should be logarithmised or not.

isLoggable(Object) - Method in class net.sf.basedb.core.log.db.DbLogManagerFactory

isLoggable(Object) - Method in interface net.sf.basedb.core.log.LogManagerFactory

Checks if changes to the given entity should be logged or not.

isLoggedIn() - Method in class net.sf.basedb.core.SessionControl

Checks if a user is logged in or not.

isLogging() - Method in class net.sf.basedb.core.plugin.AbstractPlugin

Checks if logging is enabled.

isLoggingDetailedProperties() - Method in class net.sf.basedb.core.log.db.DbLogManagerFactory

Should individual log entries for each changed property be created or not?

isLoggingOldPropertyValues() - Method in class net.sf.basedb.core.log.db.DbLogManagerFactory

Should log entries with old property values be created or not?

isMandatory - Variable in class net.sf.basedb.core.ClonableProperty

isMandatory() - Method in class net.sf.basedb.core.ClonableProperty

Check if this property is mandatory in all clone templates.

isMandatory() - Method in class net.sf.basedb.core.data.ReporterClonePropertyData

If the column is a mandatory that must be in all clone templates.

isMasked() - Method in class net.sf.basedb.core.data.ParameterValueData

A flag indicating if the value should be masked when displayed in client applications (eg. since it may be a password) NOTE!

isMasked() - Method in class net.sf.basedb.core.ParameterInfo

Should this parameter be masked in the GUI?

isMasked() - Method in class net.sf.basedb.core.ParameterType

Should this parameter be masked in the GUI?

isMasked() - Method in class net.sf.basedb.core.PasswordParameterType

isMember(AnnotationTypeCategory) - Method in class net.sf.basedb.core.AnnotationType

Checks if the annotation type is a member of a category.

isMember(Group) - Method in class net.sf.basedb.core.Group

Checks if a group is a member of this group.

isMember(Listable) - Method in class net.sf.basedb.core.ItemList

Check if the given item is a member of this list.

isMember(User) - Method in class net.sf.basedb.core.Group

Checks if a user is a member of this group.

isMember(User) - Method in class net.sf.basedb.core.Role

Check if the given user is member of this role or not.

isMemberOf(Group) - Method in class net.sf.basedb.core.SessionControl

Check if the logged in user is a member, directly or indirectly, of the specified group.

isMemberOf(Project) - Method in class net.sf.basedb.core.SessionControl

Check if the logged in user is a member, directly or indirectly, of the specified project.

isMemberOf(Role) - Method in class net.sf.basedb.core.SessionControl

Check if the logged in user is a member of the specified role.

isModified() - Method in class net.sf.basedb.core.hibernate.SchemaGenerator.SqlStatement

isMultiHop() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

If the property starts with a '/' it is a multi-hop specification.

isMultiple() - Method in class net.sf.basedb.plugins.executor.ParameterDefinition

Can this parameter have multiple values or only one?

isMultiuserAccount() - Method in class net.sf.basedb.core.data.UserData

Check if this account has enabled the multiuser feature.

isMultiuserAccount() - Method in class net.sf.basedb.core.User

Check if the user account is a multiuser account or not.

isNegationOperator - Variable in enum class net.sf.basedb.core.Operator

isNegationOperator() - Method in enum class net.sf.basedb.core.Operator

Negation operators typically need to handle 'null' checks a bit differently.

isNew - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile

isNew() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile

If the file is a new file not previously processed by the extension system.

isNewitem() - Method in class net.sf.basedb.clients.web.taglib.Select

isNotFound() - Method in class net.sf.basedb.util.extensions.xml.PluginInfo

Does this plug-in exists on the server or not?

isNotLoggable(String) - Method in class net.sf.basedb.core.log.EntityLogOptions

Check if the method corresponding to the given property name has been annotated with the NotLoggable annotation or not.

isNotPartOf(String, String, ReporterList) - Static method in class net.sf.basedb.core.query.Hql

isNotPartOf(ReporterList) - Static method in class net.sf.basedb.core.query.Dynamic

isNullable - Variable in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo

isNullable() - Method in class net.sf.basedb.core.data.ReporterClonePropertyData

If the column is nullable or not.

isNullable() - Method in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo

isNullable() - Method in class net.sf.basedb.core.ExtendedProperty

Check if the property allows null values or not.

isNullable() - Method in class net.sf.basedb.core.VirtualColumn

If null values are allowed in the column or not.

isNumerical - Variable in enum class net.sf.basedb.core.Type

isNumerical() - Method in enum class net.sf.basedb.core.Type

If the values of this type are numerical values.

isOld() - Method in class net.sf.basedb.core.DiskUsageStatistics.Summary

Check if this summary object is old by comparing it's age to the DiskUsageStatistics.getMaxAge().

isOnlyDirty(String) - Method in class net.sf.basedb.core.log.EntityDetails

Checks if the given property is the only modified property.

isOpen() - Method in class net.sf.basedb.core.hibernate.SessionWrapper

isOpen() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

isOperator() - Method in class net.sf.basedb.util.jep.convert.AbstractJepConversionFunction

isOperator() - Method in class net.sf.basedb.util.jep.convert.AddConverter

isOperator() - Method in class net.sf.basedb.util.jep.convert.AndConverter

isOperator() - Method in class net.sf.basedb.util.jep.convert.DivideConverter

isOperator() - Method in class net.sf.basedb.util.jep.convert.EqualsConverter

isOperator() - Method in class net.sf.basedb.util.jep.convert.GreaterConverter

isOperator() - Method in class net.sf.basedb.util.jep.convert.GreaterEqualsConverter

isOperator() - Method in interface net.sf.basedb.util.jep.convert.JepConversionFunction

If this converter is a built-in operator.

isOperator() - Method in class net.sf.basedb.util.jep.convert.LessConverter

isOperator() - Method in class net.sf.basedb.util.jep.convert.LessEqualsConverter

isOperator() - Method in class net.sf.basedb.util.jep.convert.MultiplyConverter

isOperator() - Method in class net.sf.basedb.util.jep.convert.NotConverter

isOperator() - Method in class net.sf.basedb.util.jep.convert.NotEqualsConverter

isOperator() - Method in class net.sf.basedb.util.jep.convert.OrConverter

isOperator() - Method in class net.sf.basedb.util.jep.convert.SubtractConverter

isOperator() - Method in class net.sf.basedb.util.jep.convert.UMinusConverter

Convert to expression by calling Expressions.negate(Expression).

isOutDated(boolean) - Method in class net.sf.basedb.clients.web.extensions.XJspCompiler

Checks if the extensions JAR file has been modified.

isOverridingDefault() - Method in class net.sf.basedb.core.Annotation

Is this (project-specific) annotation overriding a default value?

isOwner() - Method in interface net.sf.basedb.core.Ownable

Check if the logged in user is the owner of this item or not.

isOwner() - Method in class net.sf.basedb.core.OwnedItem

isPackageDefined(String) - Method in class net.sf.basedb.util.JarClassLoader

isParameter(Annotation) - Method in class net.sf.basedb.core.Protocol

Check if the annotation is parameter to this protocol.

isParameter(AnnotationType) - Method in class net.sf.basedb.core.Protocol

Check if the annotation type is a parameter to this protocol.

isParticipant(BioPlate) - Method in class net.sf.basedb.core.BioPlateEvent

Check if the given bioplate is a participant of this event.

isPartOf(String, String, ReporterList) - Static method in class net.sf.basedb.core.query.Hql

isPartOf(ReporterList) - Static method in class net.sf.basedb.core.query.Dynamic

isPaused() - Method in class net.sf.basedb.util.jobagent.JobAgentInfo

If the job agent is paused or running.

isPermanent() - Method in class net.sf.basedb.core.query.QueryParameter

Check if the parameter is a permanent parameter.

isPlateEvent() - Method in class net.sf.basedb.core.BioMaterialEvent

Check if this event is related with a bioplate event.

isPlatform(String) - Method in class net.sf.basedb.core.ArrayDesign

Check if the platform/variant of this array design has the given external ID.

isPlatform(String) - Method in class net.sf.basedb.core.RawBioAssay

Check if the platform/variant of this raw bioassay has the given external ID.

isPlatformFile() - Method in class net.sf.basedb.core.FileSetMember

Checks if this file is part of the platform/variant the parent item belongs to.

isPrimaryKey() - Method in class net.sf.basedb.core.VirtualColumn

If the column is part of the primary key or not.

isProjectSpecific() - Method in class net.sf.basedb.core.Annotation

Is this annotation a project-specific annotation?

isPropertyPathProtected(String) - Method in class net.sf.basedb.core.log.EntityLogOptions

Check if the method corresponding to the given property name has been annotated with the PropertyPathProtected annotation or not.

isProtocolParameter - Variable in class net.sf.basedb.core.data.AnnotationTypeData

isProtocolParameter() - Method in class net.sf.basedb.core.AnnotationType

If this annotation type is intended to be used as a protocol parameter or as a regular annotations.

isProtocolParameter() - Method in class net.sf.basedb.core.data.AnnotationTypeData

If this annotation type is intended to be used as a protocol parameter or as a regular annotation.

isProtocolParameter(Protocol) - Method in class net.sf.basedb.core.AnnotationType

Check if this annotation type is a parameter to the specified protocol.

isPublic - Variable in class net.sf.basedb.core.data.ContextData

isPublic() - Method in class net.sf.basedb.core.data.ContextData

If the settings are public (ie. can be used by anyone) or not.

isQuotaLimited() - Method in enum class net.sf.basedb.core.Location

A flag indicating if a file that is stored at this location should be included in quota limit.

isRead - Variable in class net.sf.basedb.core.data.MessageData

isRead() - Method in class net.sf.basedb.core.data.MessageData

Check if the message has been read or not.

isRead() - Method in class net.sf.basedb.core.Message

Check if the message has been read or not.

isReadonly() - Method in class net.sf.basedb.core.AbstractHqlQuery

isReadonly() - Method in class net.sf.basedb.core.AbstractQuery

isReadonly() - Method in class net.sf.basedb.core.DynamicRawDataQuery

isReadonly() - Method in class net.sf.basedb.core.DynamicReporterQuery

isReadonly() - Method in interface net.sf.basedb.core.query.Query

If this query is readonly and cannot be structurally modified.

isReadOnly() - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

isReadOnly(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

isRegistrationDelayed() - Method in class net.sf.basedb.util.extensions.manager.processor.IgnoreFileProcessor

Is the actual registration delayed or not?

isRegistrationDelayed() - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor

Is the actual registration delayed or not?

isRelated(DbControl, OverviewContext, Extract, Extract) - Static method in class net.sf.basedb.util.overview.validator.ExtractValidator

Check if two given extracts have a parent-child relationship.

isRemoved() - Method in class net.sf.basedb.core.BioAssaySet

isRemoved() - Method in class net.sf.basedb.core.BioPlateEventType

isRemoved() - Method in class net.sf.basedb.core.BioPlateType

isRemoved() - Method in class net.sf.basedb.core.CommonItem

isRemoved() - Method in class net.sf.basedb.core.DataFileType

isRemoved() - Method in class net.sf.basedb.core.Directory

isRemoved() - Method in class net.sf.basedb.core.ExtraValueType

isRemoved() - Method in class net.sf.basedb.core.Group

isRemoved() - Method in class net.sf.basedb.core.ItemSubtype

isRemoved() - Method in class net.sf.basedb.core.Message

isRemoved() - Method in class net.sf.basedb.core.MimeType

isRemoved() - Method in class net.sf.basedb.core.News

isRemoved() - Method in class net.sf.basedb.core.PlateEventType

isRemoved() - Method in class net.sf.basedb.core.PlateGeometry

isRemoved() - Method in class net.sf.basedb.core.Platform

isRemoved() - Method in class net.sf.basedb.core.PlatformVariant

isRemoved() - Method in class net.sf.basedb.core.PluginDefinition

isRemoved() - Method in class net.sf.basedb.core.PluginType

isRemoved() - Method in class net.sf.basedb.core.Project

isRemoved() - Method in class net.sf.basedb.core.Quantity

isRemoved() - Method in class net.sf.basedb.core.Quota

isRemoved() - Method in interface net.sf.basedb.core.Removable

Check if the removed flag is set for this item.

isRemoved() - Method in class net.sf.basedb.core.ReporterType

isRemoved() - Method in class net.sf.basedb.core.Role

isRemoved() - Method in class net.sf.basedb.core.Transformation

isRemoved() - Method in class net.sf.basedb.core.Unit

isRemoved() - Method in class net.sf.basedb.core.User

isRemoved() - Method in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter

isReporterField() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField

isReporterField() - Method in class net.sf.basedb.plugins.BfsExporterPlugin.ExtendedExportableField

isRequired() - Method in class net.sf.basedb.clients.web.taglib.Select

isRequired() - Method in class net.sf.basedb.core.data.ItemSubtypeFileTypeData

If a file of this type is required or not.

isRequired() - Method in class net.sf.basedb.core.data.PlatformFileTypeData

If a file of this type is required or not.

isRequired() - Method in class net.sf.basedb.core.ItemSubtypeFileType

Check if a file of this type is required or not.

isRequired() - Method in class net.sf.basedb.core.PlatformFileType

Check if a file of this type is required or not.

isRequired() - Method in interface net.sf.basedb.core.UsableDataFileType

A flag indicating if a file should be required or not.

isRequired() - Method in class net.sf.basedb.plugins.executor.ParameterDefinition

Is this parameter a required parameter or not?

isRequiredForMiame() - Method in class net.sf.basedb.core.AnnotationType

Check an annotation of this annotation type required for an item to be compliant with the MIAME recommendation.

isRequiredForMiame() - Method in class net.sf.basedb.core.data.AnnotationTypeData

If an annotation of this type must be present for an annotatable item to be compliant with MIAME.

isRestrictedEdit() - Method in class net.sf.basedb.core.ExtendedProperty

Check if the value of this property is restricted for editing or not.

isReturningTotalCount() - Method in class net.sf.basedb.core.AbstractQuery

isReturningTotalCount() - Method in interface net.sf.basedb.core.query.Query

If this query returns the total count or not.

isRoleInactive(int) - Method in class net.sf.basedb.core.SessionControl

Is the given role inactive or not?

isRolledBack - Variable in class net.sf.basedb.core.DbControl

If the current transaction has been rolled back or not.

isRolledBack() - Method in class net.sf.basedb.core.DbControl

If the transaction was rolled back, either as a call to DbControl.close() or because of an error during DbControl.commit().

isRoot - Variable in class net.sf.basedb.core.data.DerivedBioAssayData

isRoot() - Method in class net.sf.basedb.core.data.DerivedBioAssayData

A flag indicating if this is a root derived bioassay or not.

isRoot() - Method in class net.sf.basedb.core.DerivedBioAssay

Check if this bioassay set is derived from one or more physical bioassays or from derived bioassays.

isRootDirectory() - Method in class net.sf.basedb.core.Directory

Returns TRUE if this directories parent equals null and therfore is a root directory.

isRunning - Variable in class net.sf.basedb.clients.jobagent.Agent

isRunning - Static variable in class net.sf.basedb.core.Application

If BASE is running or not.

isRunning - Variable in class net.sf.basedb.core.File.CharsetTesterThread

isRunning - Variable in class net.sf.basedb.util.timer.PerformanceTimer

isRunning() - Method in class net.sf.basedb.clients.jobagent.Agent

Check if the job agent is running or not.

isRunning() - Method in class net.sf.basedb.clients.web.extensions.service.DummyService

isRunning() - Method in interface net.sf.basedb.clients.web.extensions.service.ServiceControllerAction

Is the service running or not?

isRunning() - Static method in class net.sf.basedb.core.Application

Check if BASE is running.

isRunning(int) - Method in class net.sf.basedb.util.timer.PerformanceTimer

Check if a timer is running or not.

isSameArrayDesign(ArrayDesign) - Method in class net.sf.basedb.core.RawBioAssay

Checks if the given array design is the same as already set on this raw bioassay.

isSearchingInheritedAnnotations() - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil

Is this loader searching for inherited annotations?

isSearchingPrimaryAnnotations() - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil

Is this loader searching for primary annotations?

isSelectionMode() - Method in class net.sf.basedb.clients.web.ModeInfo

isShared() - Method in interface net.sf.basedb.core.Shareable

Check if this item has been shared or not.

isShared() - Method in class net.sf.basedb.core.SharedItem

isSkip() - Method in class net.sf.basedb.clients.web.taglib.table.Hidden

isSnapshotInvalid() - Method in class net.sf.basedb.core.AnnotationSet

Get the status of the 'invalid snapshot' flag.

isSortable() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

isSortable() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction

A flag to indicate if sorting by this column is enabled for not.

isSortable() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

isSource(BioMaterial) - Method in class net.sf.basedb.core.BioMaterialEvent

Check if the given biomaterial has been used as a source in this event.

isStateless() - Method in class net.sf.basedb.core.AbstractHqlQuery

If queries are using the stateless Hibernate session or the regular session.

isSticky() - Method in class net.sf.basedb.core.data.NewsData

Sticky news should be sorted before non-sticky news regardless of the date.

isSticky() - Method in class net.sf.basedb.core.News

Sticky news items should be sorted before non-sticky ones, but that is up to the client application to implement.

isStoredInDb() - Method in class net.sf.basedb.core.RawDataType

If the raw data of this raw data type can be stored in the database or not.

isStringType() - Method in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo

isSymmetrical() - Method in interface net.sf.basedb.util.encode.EncoderDecoder

isSymmetrical() - Method in class net.sf.basedb.util.encode.IdentityEncoderDecoder

isSymmetrical() - Method in class net.sf.basedb.util.encode.TabCrLfEncoderDecoder

isSymmetrical() - Method in class net.sf.basedb.util.encode.ToSpaceEncoderDecoder

isSystemItem() - Method in class net.sf.basedb.core.BioPlateEventType

isSystemItem() - Method in class net.sf.basedb.core.Directory

isSystemItem() - Method in class net.sf.basedb.core.Group

isSystemItem() - Method in class net.sf.basedb.core.ItemSubtype

isSystemItem() - Method in class net.sf.basedb.core.Quantity

isSystemItem() - Method in class net.sf.basedb.core.Quota

isSystemItem() - Method in class net.sf.basedb.core.QuotaType

isSystemItem() - Method in class net.sf.basedb.core.Role

isSystemItem() - Method in interface net.sf.basedb.core.SystemItem

Check if the item is a system item or not.

isSystemItem() - Method in class net.sf.basedb.core.User

isTemporal - Variable in enum class net.sf.basedb.core.Type

isTemporal() - Method in enum class net.sf.basedb.core.Type

If the values of this type are date/time related.

isTemporary() - Method in class net.sf.basedb.core.PropertyFilter

Is this filter a temporary filter or not.

isText - Variable in enum class net.sf.basedb.core.Type

isText() - Method in enum class net.sf.basedb.core.Type

If the values of this type are text values.

isTraceEnabled() - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLogger

Check if TRACE logging has been enabled or not.

isTransformed - Variable in enum class net.sf.basedb.core.IntensityTransform

If the intensities are transformed or not.

isTransformed() - Method in enum class net.sf.basedb.core.IntensityTransform

Does this intensity transformation represents a transformation that has modified the spot intensity values or not?

isTrulyUnique() - Method in class net.sf.basedb.plugins.batchimport.AnnotationIdMethod

isTrulyUnique() - Method in class net.sf.basedb.plugins.batchimport.FallbackIdMethod

isTrulyUnique() - Method in class net.sf.basedb.plugins.batchimport.FileImporter.PathIdMethod

isTrulyUnique() - Method in interface net.sf.basedb.plugins.batchimport.IdMethod

If the identification method is truly unique or not.

isTrulyUnique() - Method in class net.sf.basedb.plugins.batchimport.InternalIdMethod

isTrulyUnique() - Method in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod

isTrulyUnique() - Method in class net.sf.basedb.plugins.batchimport.PropertyIdMethod

isTrusted() - Method in class net.sf.basedb.core.data.JobAgentSettingsData

If the plugin should be trusted or not.

isTrusted() - Method in class net.sf.basedb.core.data.PluginDefinitionData

If the plugin should be trusted or not.

isTrusted() - Method in class net.sf.basedb.core.JobAgentSettings

If the plugin is a trusted plugin or not.

isTrusted() - Method in class net.sf.basedb.core.PluginDefinition

If this plugin is trusted or not.

isUnique - Variable in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo

isUnique - Variable in class net.sf.basedb.core.dbengine.TableInfo.IndexInfo

isUnique() - Method in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo

isUnique() - Method in class net.sf.basedb.core.dbengine.TableInfo.IndexInfo

isUnique() - Method in class net.sf.basedb.core.VirtualColumn

If the column must contain unique values or not.

isUnique(String) - Method in class net.sf.basedb.util.bfs.AbstractDataWriterFactory

Checks if the suggested file name has already been used by this data writer factory or not.

isUnique(String) - Method in class net.sf.basedb.util.bfs.AbstractFilenameGenerator

Checks if the suggested file name has already been generated by this file name generator or not.

isUnsafeInlineScriptsAllowed() - Static method in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter

Checks if the current policy allows 'unsafe-inline' for the 'script-src' attribute.

isUpdateable() - Method in class net.sf.basedb.core.ExtendedProperty

Check if the value of this property should be updated in the database when an item is updated.

isUpToDate() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

A primary or inherited annotation is always up-to-date.

isUsableUnit(Unit) - Method in class net.sf.basedb.core.AnnotationType

Checks if the given unit is a unit that has been specified as a "usable" unit for this annotation type.

isUsed() - Method in class net.sf.basedb.core.AnnotationSet

Always return TRUE.

isUsed() - Method in class net.sf.basedb.core.AnnotationType

Checks if: Annotations of this type exists Experiments are using this annotation type as an experimental factor Protocols are using this annotation type as a protocol parameter

isUsed() - Method in class net.sf.basedb.core.AnyToAny

Always FALSE.

isUsed() - Method in class net.sf.basedb.core.ArrayBatch

isUsed() - Method in class net.sf.basedb.core.ArrayDesign

isUsed() - Method in class net.sf.basedb.core.ArrayDesignBlock

Array design blocks are always used by an array design.

isUsed() - Method in class net.sf.basedb.core.ArrayDesignPlate

Always TRUE.

isUsed() - Method in class net.sf.basedb.core.ArraySlide

isUsed() - Method in class net.sf.basedb.core.BasicItem

Check if this item is used by some other item.

isUsed() - Method in class net.sf.basedb.core.BioPlate

Check if there are any MeasuredBioMaterial on this plate.

isUsed() - Method in class net.sf.basedb.core.BioPlateEventType

Check if there are any BioPlateEvents using this type.

isUsed() - Method in class net.sf.basedb.core.BioPlateType

Check if there are any BioPlates or BioPlateEventDefinitions using this type.

isUsed() - Method in class net.sf.basedb.core.BioSource

Check that: no Sample has been created from this biosource

isUsed() - Method in class net.sf.basedb.core.BioWell

Check if a MeasuredBioMaterial is linked to this bio-well

isUsed() - Method in class net.sf.basedb.core.DataFileType

Check if: A file has been tagged with this type in a file set A platform is using this file type

isUsed() - Method in class net.sf.basedb.core.DerivedBioAssay

isUsed() - Method in class net.sf.basedb.core.Directory

Check that: no files are in the directory no subdirectories are in the directory no user has this directory as the home directory

isUsed() - Method in class net.sf.basedb.core.DiskUsage

isUsed() - Method in class net.sf.basedb.core.Extract

Check that: no PhysicalBioAssay:s has been created from this item no Extract:s has been created from this item no DerivedBioAssay is referencing this item no RawBioAssay is referencing this item

isUsed() - Method in class net.sf.basedb.core.ExtraValueType

Check if: Any ExtraValue:s of this type exists

isUsed() - Method in class net.sf.basedb.core.File

Checks if: A FileAttachable item is using this key.

isUsed() - Method in class net.sf.basedb.core.FileServer

Checks if there are files registered with this server.

isUsed() - Method in class net.sf.basedb.core.FileSet

Always return TRUE.

isUsed() - Method in class net.sf.basedb.core.Group

Checks if: A user has been assigned this group as a quota group There are also other items that can reference a group: DiscUsage Other groups ItemKeys Projects Users (as group members) The links to all these items are automatically deleted if the group is deleted and aren't included in this check.

isUsed() - Method in class net.sf.basedb.core.Hardware

Check if: a DerivedBioAssay is linked to this hardware an ArrayBatch is linked to this hardware a BioMaterialEvent is linked to this hardware a PlateEvent is linked to this hardware

isUsed() - Method in class net.sf.basedb.core.ItemKey

Checks if: A Shareable item is using this key.

isUsed() - Method in class net.sf.basedb.core.ItemSubtype

Checks if: any Subtypable item is using this subtype.

isUsed() - Method in class net.sf.basedb.core.Job

Return TRUE if the status is EXECUTING or: a transformation is linked to this job a raw bioassay is linked to this job an array design is linked to this job FALSE otherwise.

isUsed() - Method in class net.sf.basedb.core.Kit

Check if: a BioMaterialEvent is linked to this kit a BioPlateEvent is linked to this kit

isUsed() - Method in class net.sf.basedb.core.MeasuredBioMaterial

Check that: no pooled biomaterial has been created from this item

isUsed() - Method in class net.sf.basedb.core.PermissionTemplate

Check if: A Project uses this template

isUsed() - Method in class net.sf.basedb.core.PhysicalBioAssay

Check that: No DerivedBioAssay:s use the physical bioassay

isUsed() - Method in class net.sf.basedb.core.Plate

Check if: another Plate has been created from this one (via a PlateMapping) any ArrayDesign:s are using this plate Wells are deleted automatically.

isUsed() - Method in class net.sf.basedb.core.PlateEventType

Check if: A PlateEvent of this type exists

isUsed() - Method in class net.sf.basedb.core.PlateGeometry

Check if: A PlateType with this geometry exists A PlateMapping to/from this geometry exists A BioPlate that uses this geometry exists

isUsed() - Method in class net.sf.basedb.core.PlateMapping

Check if: A Plate has been created from this mapping

isUsed() - Method in class net.sf.basedb.core.PlateType

Check if: Any Plate:s of this type exists

isUsed() - Method in class net.sf.basedb.core.Platform

Check if: any raw bioassays or array design are using this platform

isUsed() - Method in class net.sf.basedb.core.PlatformVariant

Check if: any raw bioassays or array design are using this platform variant

isUsed() - Method in class net.sf.basedb.core.PluginConfiguration

Check if: A Job is using this plugin configuration

isUsed() - Method in class net.sf.basedb.core.PluginDefinition

Check if a PluginConfiguration is using this definition.

isUsed() - Method in class net.sf.basedb.core.ProjectKey

Checks if: A Shareable item is using this key.

isUsed() - Method in class net.sf.basedb.core.Protocol

Check if this protocol is used by: a BioMaterialEvent a PlateEvent an ArrayBatch a DerivedBioAssay a RawBioAssay

isUsed() - Method in class net.sf.basedb.core.Quantity

Check if: Units for this quantity exists.

isUsed() - Method in class net.sf.basedb.core.Quota

Checks if: a Group has been assigned this quota a User has been assigned this quota

isUsed() - Method in class net.sf.basedb.core.QuotaType

isUsed() - Method in class net.sf.basedb.core.RawBioAssay

Check if: An Experiment is using this raw bioassay A Transformation is using this raw bio raw data type will also be updated.

isUsed() - Method in class net.sf.basedb.core.ReporterCloneTemplate

Check if: An experiment/virtualdb is using this template

isUsed() - Method in class net.sf.basedb.core.ReporterType

Check if any reporters of this type exists.

isUsed() - Method in class net.sf.basedb.core.RoleKey

Always return TRUE.

isUsed() - Method in class net.sf.basedb.core.Sample

Check that: no Extract:s has been created from this item no Sample:s has been created from this item

isUsed() - Method in class net.sf.basedb.core.Software

Check if: a RawBioAssay was created with this software a DerivedBioassay was created with this software

isUsed() - Method in class net.sf.basedb.core.Tag

Check if: Some Extract:s are marked with this tag

isUsed() - Method in class net.sf.basedb.core.Unit

Check if: Annotation types are using this unit as default unit Annotations are using this unit

isUsed() - Method in class net.sf.basedb.core.User

Checks if: any Ownable item is owned by this user A user can also be referenced from groups, roles, projects, item keys, sessions and settings, but those references are automatically deleted if the user is deleted and aren't inclued in this check.

isUsed() - Method in class net.sf.basedb.core.Well

Check if: a Feature is linked to this well another Well has this well as it's parent well

isUsedByOther(PhysicalBioAssay) - Method in class net.sf.basedb.core.ArraySlide

Checks if this array slide is used by a different bioassay than the given one.

isUsedKey(String) - Method in class net.sf.basedb.util.bfs.MetadataWriter

Checks if the current section already has an entry for the given key or not.

isUsing(RawBioAssay) - Method in class net.sf.basedb.core.Experiment

Check if a raw bioassay is used in this experiment.

isUsingColors() - Method in class net.sf.basedb.core.Coloring

If this item should be colored or not.

isUsingColors() - Method in class net.sf.basedb.core.data.ColoringData

If colors should be used or not.

isUsingNonRemovableItem(Set<ItemProxy>) - Method in class net.sf.basedb.core.Trashcan.CircularRefInfo

Check if all using items of the main items is found among the 'itemsToRemove'.

isUsingTo() - Method in class net.sf.basedb.core.AnyToAny

If this link counts as using the destination item.

isUsingTo() - Method in class net.sf.basedb.core.data.AnyToAnyData

If the link counts as using the item we are linking to.

isValid - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile

isValid - Variable in class net.sf.basedb.util.fileset.ValidationRenderer

isValid() - Method in class net.sf.basedb.core.data.FileSetMemberData

If the file has been validated or not.

isValid() - Method in class net.sf.basedb.core.FileSetMember

Check if the file has been validated and if it passed or not.

isValid() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile

Is the file a valid extensions file according to the last performed validation.

isValidColumnName(String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine

Checks that the name only contains the following characters: a-zA-Z0-9_ It must also start with a letter or underscore.

isValidColumnName(String) - Method in interface net.sf.basedb.core.dbengine.DbEngine

Check if a given string is valid to be used as a column name in the current database.

isValidEmail(String) - Static method in class net.sf.basedb.clients.web.util.HTML

Checks if the given string looks like an email address.

isValidEmail(String) - Static method in class net.sf.basedb.util.EmailUtil

Checks if the given string looks like an email address.

isValidKey(String) - Static method in class net.sf.basedb.util.StaticCache

Checks if the given key is a vilid cache entry key.

isValidName(String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine

Check that the name only contains a-zA-Z0-9_ and starts with a letter or underscore.

isValidName(String) - Static method in class net.sf.basedb.core.ExtendedProperty

Check that the name only contains a-zA-Z0-9_ and starts with a letter or underscore.

isValidName(String) - Static method in class net.sf.basedb.core.Path

Check if a name is valid as a partial path name, ie. it must not contain any of the characters in Path.INVALID_CHARACTERS.

isValidSoFar - Variable in class net.sf.basedb.util.fileset.ValidatingFileSetMember

isValidSoFar() - Method in class net.sf.basedb.util.fileset.ValidatingFileSetMember

Is the member considered valid so far in the validation process?

isValidTableName(String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine

Checks that the name only contains the following characters: a-zA-Z0-9_ It must also start with a letter or underscore.

isValidTableName(String) - Method in interface net.sf.basedb.core.dbengine.DbEngine

Check if a given string is valid to be used as a table name in the current database.

isValidUrl(String) - Static method in class net.sf.basedb.clients.web.util.HTML

Checks if the given string looks like an URL.

isVerbose - Variable in class net.sf.basedb.core.hibernate.DbIndexWork

isVerified - Variable in class net.sf.basedb.core.data.UserDeviceData

isVerified() - Method in class net.sf.basedb.core.data.UserDeviceData

This flag is TRUE if the device has been verified (by sending a code via email).

isVerified() - Method in class net.sf.basedb.core.UserDevice

Has this device been verified or not?

isVerifyOnly() - Method in class net.sf.basedb.core.authentication.LoginRequest

If this flag is set, the login parameters are only verified and the actual login is aborted.

isVertical() - Method in class net.sf.basedb.clients.web.taglib.menu.Menu

isVisible() - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

isVisible() - Method in interface net.sf.basedb.clients.web.extensions.menu.MenuItemAction

If the menu item should be visible or not.

isVisible() - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean

isVisible() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory

isVisible() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab

isVisible() - Method in interface net.sf.basedb.clients.web.extensions.tabcontrol.TabAction

If the tab should be visible or not.

isVisible() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean

isVisible() - Method in interface net.sf.basedb.clients.web.extensions.toolbar.ButtonAction

If the button should be visible or not.

isVisible() - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean

isVisible() - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory

isVisible() - Method in class net.sf.basedb.clients.web.taglib.Button

isVisible() - Method in class net.sf.basedb.clients.web.taglib.Help

isVisible() - Method in class net.sf.basedb.clients.web.taglib.HideableSection

isVisible() - Method in class net.sf.basedb.clients.web.taglib.Icon

isVisible() - Method in class net.sf.basedb.clients.web.taglib.Input

isVisible() - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem

isVisible() - Method in class net.sf.basedb.clients.web.taglib.menu.Menuseparator

isVisible() - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu

isVisible() - Method in class net.sf.basedb.clients.web.taglib.path.PathElement

isVisible() - Method in class net.sf.basedb.clients.web.taglib.Select

isVisible() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab

isVisible() - Method in class net.sf.basedb.clients.web.taglib.table.Button.ButtonActionWrapper

isVisible() - Method in class net.sf.basedb.clients.web.taglib.table.Button

isVisible() - Method in class net.sf.basedb.clients.web.taglib.table.Cell

isVisible() - Method in class net.sf.basedb.clients.web.taglib.table.Header

isVisible() - Method in class net.sf.basedb.clients.web.taglib.table.Label

isVisible() - Method in class net.sf.basedb.clients.web.taglib.table.Navigator

isVisible() - Method in class net.sf.basedb.clients.web.taglib.table.Panel

isVisible() - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector

isVisible() - Method in class net.sf.basedb.clients.web.taglib.table.Row

isVisible() - Method in class net.sf.basedb.clients.web.taglib.table.Toolbar

isVisible() - Method in class net.sf.basedb.clients.web.taglib.Zoom

isWriteProtected() - Method in class net.sf.basedb.core.data.FileData

If the actual file contents should be write protected or not.

isWriteProtected() - Method in class net.sf.basedb.core.File

Check if the file data is write protected.

isWriteProtected() - Method in class net.sf.basedb.core.ParameterValuesImpl

isWritingData() - Method in class net.sf.basedb.util.basefile.BaseFileWriter

isWritingHeaders() - Method in class net.sf.basedb.util.basefile.BaseFileWriter

isXJsp - Variable in class net.sf.basedb.clients.web.extensions.XJspCompiler

it - Variable in class net.sf.basedb.core.FastAnnotationLoader.FastIterator

item - Variable in class net.sf.basedb.clients.web.taglib.extensions.Render

item - Variable in class net.sf.basedb.clients.web.taglib.PropertyValue

The item.

item - Variable in class net.sf.basedb.clients.web.taglib.SubtypeSelector

item - Variable in class net.sf.basedb.clients.web.taglib.table.ExtensionCells

item - Variable in class net.sf.basedb.core.AnnotationSet

The item this annotation set belongs to.

item - Variable in class net.sf.basedb.core.Coloring

item - Variable in class net.sf.basedb.core.ContextKey

item - Variable in class net.sf.basedb.core.DbControl.SaveIf

item - Variable in class net.sf.basedb.core.DiskUsage

The item this diks usage information belongs to.

item - Variable in class net.sf.basedb.core.FileSet

The item this file set belongs to.

item - Variable in class net.sf.basedb.core.log.ManualLogEntry

item - Variable in class net.sf.basedb.core.plugin.GuiContext

item - Variable in class net.sf.basedb.core.query.HqlEntityExpression

item - Variable in class net.sf.basedb.core.SessionControl.MainContext

item - Variable in class net.sf.basedb.core.Trashcan.CircularRefInfo

item - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations

item - Variable in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper

item - Variable in class net.sf.basedb.util.extensions.ClientContext

item - Variable in class net.sf.basedb.util.overview.filter.BasicItemFilter

item - Variable in class net.sf.basedb.util.overview.Fix

item - Variable in class net.sf.basedb.util.overview.Node

item() - Method in class net.sf.basedb.core.SessionControl.MainContext

Get the item of this main context.

item(DbControl, Item, int) - Method in class net.sf.basedb.util.formatter.PropertyFilterFormatter

item(Item) - Static method in class net.sf.basedb.core.plugin.GuiContext

Shortcut to create a single-item context.

item(Item, String) - Static method in class net.sf.basedb.core.plugin.GuiContext

Shortcut to create a single-item context with a subcontext.

Item - Enum Class in net.sf.basedb.core

This class defines constants for various items in BASE.

Item(int, String, String, Class<? extends BasicItem>, Class<? extends BasicData>, Set<Permission>, float) - Constructor for enum class net.sf.basedb.core.Item

ITEM - Enum constant in enum class net.sf.basedb.core.plugin.GuiContext.Type

ITEM - Enum constant in enum class net.sf.basedb.util.overview.Node.Type

ITEM - Static variable in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil

Item.DefinedPermissions - Class in net.sf.basedb.core

Helper class to make it easier to set up the defined permissions.

ItemAlreadyExistsException - Exception in net.sf.basedb.core

This exception is thrown when trying to save an object and another object with the same ID already exists.

ItemAlreadyExistsException(String) - Constructor for exception net.sf.basedb.core.ItemAlreadyExistsException

Creates a new ItemAlreadyExistsException.

itemCache - Variable in class net.sf.basedb.core.DbControl

A cache of already loaded items.

itemCache - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

itemCache - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Cache that holds loaded/created items.

itemCache - Variable in class net.sf.basedb.util.parser.DefaultItemFunction

itemClass - Variable in enum class net.sf.basedb.core.Item

itemClass - Variable in class net.sf.basedb.core.ItemQuery

The class of the item objects that are returned.

itemClass - Variable in class net.sf.basedb.core.ItemResultIterator

The class of the items returned by the query (and this object).

itemClass - Variable in class net.sf.basedb.core.ItemResultList

The class of the items returned by the query (and this object).

itemClass - Variable in class net.sf.basedb.core.ItemResultList.ResultListIterator

itemClass - Variable in class net.sf.basedb.core.ItemResultList.ResultListListIterator

itemClassMapping - Static variable in enum class net.sf.basedb.core.Item

itemContext - Variable in class net.sf.basedb.clients.web.extensions.JspContext

ItemContext - Class in net.sf.basedb.core

This item is a helper class for client applications when they need to store information about the current context for plugins that needs to find out the current context of the running client application.

ItemContext(String, ItemContext.SortDirection, int, int) - Constructor for class net.sf.basedb.core.ItemContext

Create a new context.

ItemContext(ContextData) - Constructor for class net.sf.basedb.core.ItemContext

Create a new context from a loaded database object.

ItemContext(Item, String, String) - Constructor for class net.sf.basedb.core.ItemContext

Create a new empty context.

ItemContext(Item, ItemListSyncFilterData) - Constructor for class net.sf.basedb.core.ItemContext

Initialize the context from an item list synchronization filter.

ItemContext(Item, PropertyFilter...) - Constructor for class net.sf.basedb.core.ItemContext

Initialize the context with the special purpose of configuring a query with the given filters.

ItemContext.AddFilter - Enum Class in net.sf.basedb.core

Parameter options for ItemContext.setSubCategory(AnnotationTypeCategory, AddFilter)

ItemContext.PropertyFilterPair - Class in net.sf.basedb.core

Holds a pair of filter.

ItemContext.QueryRestrictions - Class in net.sf.basedb.core

ItemContext.RowRestrictions - Class in net.sf.basedb.core

ItemContext.SortDirection - Enum Class in net.sf.basedb.core

Enumeration used to specify the sort direction.

itemElement - Variable in class net.sf.basedb.clients.web.plugins.XMLTemplate

itemExistsErrorParameter - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

itemId - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo

itemId - Variable in class net.sf.basedb.core.data.AnnotationSetData

itemId - Variable in class net.sf.basedb.core.data.ChangeHistoryDetailData

itemId - Variable in class net.sf.basedb.core.data.ContextData

itemId - Variable in class net.sf.basedb.core.FastAnnotationLoader.FastAnnotation

The ID of the item the annotation belongs to.

itemId - Variable in class net.sf.basedb.core.ItemContext

itemId - Variable in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot

itemId - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot

itemIdPrefix - Variable in class net.sf.basedb.clients.web.plugins.XMLTemplate

itemIds - Variable in class net.sf.basedb.core.FastAnnotationLoader.FastIterator

ItemInUseException - Exception in net.sf.basedb.core

This exception is thrown when trying delete an item that is used (reference to) by some other item or items.

ItemInUseException(String) - Constructor for exception net.sf.basedb.core.ItemInUseException

Creates a new ItemInUseException.

ItemInUseException(String, Throwable) - Constructor for exception net.sf.basedb.core.ItemInUseException

Creates a new ItemInUseException with a cause.

itemIsMissing(DbControl, Item, Integer) - Method in class net.sf.basedb.core.MigrateRbaToDba.LineMapping

itemKey - Variable in class net.sf.basedb.core.data.SharedData

ItemKey - Class in net.sf.basedb.core

This class is used to get information about which users and groups a Shareable item has been shared to.

ItemKey(ItemKeyData) - Constructor for class net.sf.basedb.core.ItemKey

ITEMKEY - Enum constant in enum class net.sf.basedb.core.Item

The item is an ItemKey.

ItemKeyData - Class in net.sf.basedb.core.data

This class holds information access privileges for users and groups.

ItemKeyData() - Constructor for class net.sf.basedb.core.data.ItemKeyData

itemKeyId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba

itemKeyId - Variable in class net.sf.basedb.core.SessionControl.LoginInfo

The id of the ItemKeyData object that new items should be shared to.

itemKeys - Variable in class net.sf.basedb.core.data.GroupData

itemKeys - Variable in class net.sf.basedb.core.data.UserData

itemKeys - Variable in class net.sf.basedb.core.Keyring

A set holding all item keys, which is needed for efficient listing of shared items.

itemKeySet - Variable in class net.sf.basedb.core.SharedItem

itemList - Variable in class net.sf.basedb.core.data.ItemListSyncFilterData

itemList - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

itemList - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

itemList - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

Itemlist(Object[]) - Constructor for class net.sf.basedb.core.MigrateRbaToDba.Itemlist

ItemList - Class in net.sf.basedb.core

This class represents a list of items.

ItemList(ItemListData) - Constructor for class net.sf.basedb.core.ItemList

ITEMLIST - Enum constant in enum class net.sf.basedb.core.Item

The item is an ItemList

ItemList.DelayedAdditionManager - Class in net.sf.basedb.core

Handles items that should be added as members to the list, but since they were created in the same transaction doesn't have any ID until later in the commit phase.

ItemList.SynchronizeOption - Enum Class in net.sf.basedb.core

Options for synchronizing an existing item list with a current settings in an ItemContext.

ItemListData - Class in net.sf.basedb.core.data

This represents an arbitrary collection of items.

ItemListData() - Constructor for class net.sf.basedb.core.data.ItemListData

ItemListLoader - Class in net.sf.basedb.util.overview.loader

Node loader implementation for item lists.

ItemListLoader() - Constructor for class net.sf.basedb.util.overview.loader.ItemListLoader

ItemListMemberNameGenerator - Class in net.sf.basedb.util.overview.node

Name generator used for item list members.

ItemListMemberNameGenerator() - Constructor for class net.sf.basedb.util.overview.node.ItemListMemberNameGenerator

ItemListSyncFilterData - Class in net.sf.basedb.core.data

Synchronization options for item lists.

ItemListSyncFilterData() - Constructor for class net.sf.basedb.core.data.ItemListSyncFilterData

itemMapper - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

ItemModifiedException - Exception in net.sf.basedb.core

This exception is thrown when trying to save an item to the database that has been updated (or deleted) by another process in the meantime.

ItemModifiedException(String) - Constructor for exception net.sf.basedb.core.ItemModifiedException

Creates a new ItemModifiedException.

ItemModifiedException(StaleStateException) - Constructor for exception net.sf.basedb.core.ItemModifiedException

Create a new ItemModifiedException trying to find the item information from the Hibernate exception.

itemNotFoundErrorParameter - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

itemNotFoundErrorParameter - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

itemNotFoundErrorParameter - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

ItemNotFoundException - Exception in net.sf.basedb.core

This exception is thrown when trying to load an item from the database that does not exist.

ItemNotFoundException(String) - Constructor for exception net.sf.basedb.core.ItemNotFoundException

Creates a new ItemNotFoundException.

ItemNotFoundException(String, Throwable) - Constructor for exception net.sf.basedb.core.ItemNotFoundException

Creates a new ItemNotFoundException.

ItemParameterType<T extends BasicItem> - Class in net.sf.basedb.core

This class represent a parameter type that is an object derived from BasicData.

ItemParameterType(Class<T>, List<T>) - Constructor for class net.sf.basedb.core.ItemParameterType

Create a new item parameter type, allowing null values.

ItemParameterType(Class<T>, T, boolean, int, List<T>) - Constructor for class net.sf.basedb.core.ItemParameterType

ItemParameterValueData - Class in net.sf.basedb.core.data

Item parameter value.

ItemParameterValueData() - Constructor for class net.sf.basedb.core.data.ItemParameterValueData

ItemParameterValueData(BasicData...) - Constructor for class net.sf.basedb.core.data.ItemParameterValueData

itemPermissions - Variable in class net.sf.basedb.core.Keyring

Two-dimensional array for holding the permissions for ItemKey:s.

ItemProxy - Class in net.sf.basedb.core

ItemProxy(int, Item) - Constructor for class net.sf.basedb.core.ItemProxy

itemQuery - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

itemQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

itemQuery - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

ItemQuery<I extends BasicItem> - Class in net.sf.basedb.core

An implementation of the Query interface that returns item objects.

ItemQuery(Class<I>) - Constructor for class net.sf.basedb.core.ItemQuery

Create a new query for the specified item, using the default optional runtime filter.

ItemQuery(Class<I>, QueryRuntimeFilter) - Constructor for class net.sf.basedb.core.ItemQuery

Create a new query for the specified item, using a non-default optional runtime filter.

ItemQueryLoader<T extends BasicItem> - Class in net.sf.basedb.clients.web.plugins

A class that uses a given query to load data.

ItemQueryLoader(ItemQuery<?>, String) - Constructor for class net.sf.basedb.clients.web.plugins.ItemQueryLoader

ItemQueryWrapper - Class in net.sf.basedb.clients.web.plugins

A query wrapper for ItemQuery:s.

ItemQueryWrapper(ItemQuery<BasicItem>) - Constructor for class net.sf.basedb.clients.web.plugins.ItemQueryWrapper

Create a new query wrapper.

ItemResultIterator<I extends BasicItem> - Class in net.sf.basedb.core

Return the results of an ItemQuery as an iterator.

ItemResultIterator(ScrollIterator<? extends BasicData>, DbControl, Class<I>, long) - Constructor for class net.sf.basedb.core.ItemResultIterator

ItemResultList<I extends BasicItem> - Class in net.sf.basedb.core

Return the results of an ItemQuery as a list.

ItemResultList(List<? extends BasicData>, DbControl, Class<I>, long) - Constructor for class net.sf.basedb.core.ItemResultList

ItemResultList.ResultListIterator<T extends BasicItem> - Class in net.sf.basedb.core

Inner class to implement the iterator returned by the ItemResultList.iterator() method.

ItemResultList.ResultListListIterator<T extends BasicItem> - Class in net.sf.basedb.core

Inner class to implement the iterator returned by the ItemResultList.listIterator() method.

items - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper

items - Variable in class net.sf.basedb.core.MultiPermissions

items - Variable in class net.sf.basedb.core.ParameterType

List of allowed values.

items - Variable in class net.sf.basedb.util.annotations.RunnableInheritAnnotationsManager

ItemSubtype - Class in net.sf.basedb.core

Item subtypes can be used to classify items into sub-categories.

ItemSubtype(ItemSubtypeData) - Constructor for class net.sf.basedb.core.ItemSubtype

ITEMSUBTYPE - Enum constant in enum class net.sf.basedb.core.Item

The item is a ItemSubtype.

ItemSubtypeData - Class in net.sf.basedb.core.data

Item subtypes can be used to classify items into sub-categories.

ItemSubtypeData() - Constructor for class net.sf.basedb.core.data.ItemSubtypeData

ItemSubtypeFileType - Class in net.sf.basedb.core

This class represents a specific DataFileType that is associated with an item subtype.

ItemSubtypeFileType(ItemSubtypeFileTypeData) - Constructor for class net.sf.basedb.core.ItemSubtypeFileType

Creates a new member item from the given data.

ITEMSUBTYPEFILETYPE - Enum constant in enum class net.sf.basedb.core.Item

The item is a ItemSubtypeFileType

ItemSubtypeFileTypeData - Class in net.sf.basedb.core.data

This class hols information about which file types can be used together with item subtypes.

ItemSubtypeFileTypeData() - Constructor for class net.sf.basedb.core.data.ItemSubtypeFileTypeData

ItemSubtypeFT(ItemSubtypeData, boolean, boolean) - Constructor for class net.sf.basedb.core.Install.ItemSubtypeFT

itemSubtypes - Variable in class net.sf.basedb.core.data.DataFileTypeData

itemToCheck - Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

itemToCheck - Variable in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

itemType - Variable in class net.sf.basedb.clients.web.extensions.list.SubtypeFilter

itemType - Variable in class net.sf.basedb.clients.web.plugins.XMLTemplate

itemType - Variable in class net.sf.basedb.clients.web.taglib.SubtypeSelector

itemType - Variable in class net.sf.basedb.clients.web.taglib.table.Table

itemType - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo

itemType - Variable in class net.sf.basedb.core.AnnotationBatcher

itemType - Variable in class net.sf.basedb.core.data.AnnotationSetData

itemType - Variable in class net.sf.basedb.core.data.ChangeHistoryDetailData

itemType - Variable in class net.sf.basedb.core.data.ContextData

itemType - Variable in class net.sf.basedb.core.data.ContextIndex

itemType - Variable in class net.sf.basedb.core.data.DataFileTypeData

itemType - Variable in class net.sf.basedb.core.data.DiskUsageData

itemType - Variable in class net.sf.basedb.core.data.FileSetData

itemType - Variable in class net.sf.basedb.core.data.GuiContextData

itemType - Variable in class net.sf.basedb.core.data.ItemSubtypeData

itemType - Variable in class net.sf.basedb.core.data.RoleKeyData

itemType - Variable in class net.sf.basedb.core.DataResultIterator

The type of items returned by the query.

itemType - Variable in class net.sf.basedb.core.HibernateUtil.DelayedFilterDef

itemType - Variable in class net.sf.basedb.core.ItemContext

itemType - Variable in class net.sf.basedb.core.ItemResultIterator

The type of items returned by the query.

itemType - Variable in class net.sf.basedb.core.ItemResultList

The type of items returned by the query.

itemType - Variable in class net.sf.basedb.core.Metadata.BasicData2ItemPropertyPath

itemType - Variable in class net.sf.basedb.core.plugin.Permissions

itemType - Variable in class net.sf.basedb.core.query.HqlEntityParameterExpression

itemType - Variable in class net.sf.basedb.core.query.PermissionRestriction

itemType - Variable in class net.sf.basedb.core.query.QueryParameter

itemType - Variable in class net.sf.basedb.core.QueryRuntimeFilterManager

itemType - Variable in class net.sf.basedb.core.ReporterScoreResultIterator

The type of items returned by the query.

itemType - Variable in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot

itemType - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot

itemType - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

itemType - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

itemType - Variable in class net.sf.basedb.util.listable.PushToParentsTransformer

itemType - Variable in class net.sf.basedb.util.overview.filter.BasicItemFilter

itemType - Variable in class net.sf.basedb.util.overview.filter.ItemTypeFilter

itemType - Variable in class net.sf.basedb.util.parser.DefaultItemFunction

ItemTypeFilter - Class in net.sf.basedb.util.overview.filter

A filter implementation that mathces item types on nodes.

ItemTypeFilter(Item) - Constructor for class net.sf.basedb.util.overview.filter.ItemTypeFilter

Create a filter that finds nodes that has an attached item of the given item type.

ItemTypeFormatter - Class in net.sf.basedb.util.formatter

Formatter implementation that converts an integer into it's Item representation and the uses name() as the formatted value.

ItemTypeFormatter() - Constructor for class net.sf.basedb.util.formatter.ItemTypeFormatter

Create a new formatter.

ItemTypeFormatter(String) - Constructor for class net.sf.basedb.util.formatter.ItemTypeFormatter

Create a new formatter.

itemTypes - Variable in class net.sf.basedb.core.data.AnnotationTypeData

itemTypesColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

Column mapping parameter for "Item types".

itemTypesMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

iterate() - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

iterate() - Method in class net.sf.basedb.util.extensions.ExtensionsInvoker

Create an iterator that iterates over all Action:s created by the extensions.

iterate(DbControl) - Method in class net.sf.basedb.clients.web.plugins.DataQueryWrapper

Calls DataQuery.iterate(DbControl)

iterate(DbControl) - Method in class net.sf.basedb.clients.web.plugins.DynamicQueryWrapper

Calls AbstractSqlQuery.iterate(DbControl)

iterate(DbControl) - Method in class net.sf.basedb.clients.web.plugins.ItemQueryWrapper

Calls ItemQuery.iterate(DbControl)

iterate(DbControl) - Method in interface net.sf.basedb.clients.web.plugins.QueryWrapper

Get the ResultIterator for the query.

iterate(DbControl) - Method in class net.sf.basedb.clients.web.plugins.ReporterScoreQueryWrapper

Calls ReporterScoreQuery.iterate(DbControl)

iterate(DbControl) - Method in class net.sf.basedb.core.AbstractSqlQuery

Execute the query.

iterate(DbControl) - Method in class net.sf.basedb.core.DataQuery

Execute the query and return the results as an iterator.

iterate(DbControl) - Method in class net.sf.basedb.core.ItemQuery

Execute the query and return the results as an iterator.

iterate(DbControl) - Method in interface net.sf.basedb.core.query.SqlQuery

iterate(DbControl) - Method in class net.sf.basedb.core.ReporterScoreQuery

Execute the query and return the results as an iterator.

iterations - Variable in class net.sf.basedb.plugins.LowessNormalization.CallableWorker

iterator - Variable in class net.sf.basedb.core.ItemResultList.ResultListIterator

iterator - Variable in class net.sf.basedb.core.ItemResultList.ResultListListIterator

iterator - Variable in class net.sf.basedb.util.extensions.ActionIterator

iterator() - Method in class net.sf.basedb.core.ItemResultList

iterator() - Method in class net.sf.basedb.core.Presets

Iterate over all named presets.

iterator() - Method in class net.sf.basedb.core.Presets.Preset

Iterate over all settings.

iterator() - Method in class net.sf.basedb.util.extensions.ExtensionsInvoker

iterator() - Method in class net.sf.basedb.util.Tree

iterParameter - Static variable in class net.sf.basedb.plugins.LowessNormalization

J

JarClassLoader - Class in net.sf.basedb.util

A class loader implementation that loads classes from JAR files.

JarClassLoader(String) - Constructor for class net.sf.basedb.util.JarClassLoader

Create a new JAR file class loader.

JarClassLoader.JarClassLoaderProxy - Class in net.sf.basedb.util

A proxy class loader is typically needed when one extension depends on another extension.

JarClassLoader.JarInfo - Class in net.sf.basedb.util

JarClassLoaderProxy(String) - Constructor for class net.sf.basedb.util.JarClassLoader.JarClassLoaderProxy

Creates a proxy class loader for the given JAR file.

jarFile - Variable in class net.sf.basedb.clients.web.extensions.ServletWrapperKey

jarFile - Variable in class net.sf.basedb.core.data.PluginDefinitionData

jarFile - Variable in class net.sf.basedb.core.data.PluginTypeData

jarFile - Variable in class net.sf.basedb.util.JarClassLoader.JarInfo

jarFiles - Variable in class net.sf.basedb.util.JarClassLoader

For keeping track of jar files listed by Class-Path entry in the manifest file.

JarFirstURIComparator() - Constructor for class net.sf.basedb.util.extensions.manager.ExtensionsManager.JarFirstURIComparator

JarInfo(File) - Constructor for class net.sf.basedb.util.JarClassLoader.JarInfo

jarLoader - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile

jarPath - Variable in class net.sf.basedb.util.JarClassLoader.JarClassLoaderProxy

jarSize - Variable in class net.sf.basedb.util.JarClassLoader

The size of the JAR file.

jarTimeStamp - Variable in class net.sf.basedb.util.JarClassLoader

The timestamp of the JAR file.

javaBin - Variable in class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor

javaScriptEncode(String) - Static method in class net.sf.basedb.clients.web.util.HTML

Escape a string to make it safe for use in a JavaScript statement.

jdbcFetchSize - Static variable in class net.sf.basedb.core.HibernateUtil

Number of rows to load at a time when iterating over a result set.

jep - Variable in class net.sf.basedb.util.export.spotdata.JepDynamicField

jep - Variable in class net.sf.basedb.util.jep.FunctionSafeJep.SafeFunctionTable

jep(String, String, Type, Formula.AverageMethod, Formatter<?>) - Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory

Create a JEP dynamic field.

Jep - Class in net.sf.basedb.util.jep

Utility class for parsing mathematical expressions.

Jep() - Constructor for class net.sf.basedb.util.jep.Jep

JEP - Enum constant in enum class net.sf.basedb.core.Formula.Parser

Use the JEP parser.

JepConversionFunction<T> - Interface in net.sf.basedb.util.jep.convert

Convert a built-in JEP function or operation to a Query API Expression or Restriction.

JepDynamicField - Class in net.sf.basedb.util.export.spotdata

A dynamic field implementation that uses a JEP expression to generate the expression that is needed to select the data.

JepDynamicField() - Constructor for class net.sf.basedb.util.export.spotdata.JepDynamicField

Create a new object.

jepErrorList - Static variable in class net.sf.basedb.util.jep.Jep

jepExpression - Variable in class net.sf.basedb.clients.web.taglib.table.TableColumn

JepExpressionFunction - Interface in net.sf.basedb.util.jep

This interface should be implemented by JEP functions that can also be converted into an Expression that can be used in queries.

JepExtraValueCalculator - Class in net.sf.basedb.plugins

This plugin caluclates extra values from a bioassayset using mathematical formulas entered by the user.

JepExtraValueCalculator() - Constructor for class net.sf.basedb.plugins.JepExtraValueCalculator

JepFunction - Interface in net.sf.basedb.util.jep

This interface should be implemented by objects that can perform some kind of calculation for a JEP expression.

JepIntensityCalculatorImpl(JEP[], RawFunction, MeanFunction) - Constructor for class net.sf.basedb.util.IntensityCalculatorUtil.JepIntensityCalculatorImpl

JepIntensityTransformer - Class in net.sf.basedb.plugins

This plugin transform channel intensities using mathematical formulas entered by the user.

JepIntensityTransformer() - Constructor for class net.sf.basedb.plugins.JepIntensityTransformer

Constructor should be empty.

JepMapper - Class in net.sf.basedb.util.parser

A mapper that uses Jep to calculate the final value.

JepMapper(String, List<String>) - Constructor for class net.sf.basedb.util.parser.JepMapper

Create a new JepMapper.

JepMapper(String, List<String>, NumberFormat) - Constructor for class net.sf.basedb.util.parser.JepMapper

Deprecated.

In 3.15, use JepMapper(String, List, NumberFormat, Formatter, boolean, JepFunction...) instead

JepMapper(String, List<String>, NumberFormat, boolean) - Constructor for class net.sf.basedb.util.parser.JepMapper

Deprecated.

In 3.15, use JepMapper(String, List, NumberFormat, Formatter, boolean, JepFunction...) instead

JepMapper(String, List<String>, NumberFormat, boolean, JepFunction...) - Constructor for class net.sf.basedb.util.parser.JepMapper

Deprecated.

In 3.15, use JepMapper(String, List, NumberFormat, Formatter, boolean, JepFunction...) instead

JepMapper(String, List<String>, NumberFormat, Formatter<Date>, boolean, JepFunction...) - Constructor for class net.sf.basedb.util.parser.JepMapper

JepRestrictionFunction - Interface in net.sf.basedb.util.jep

This interface should be implemented by JEP functions that can also be converted into a Restriction that can be used in queries.

jeps - Variable in class net.sf.basedb.util.IntensityCalculatorUtil.JepIntensityCalculatorImpl

jepToExpression(JEP) - Static method in class net.sf.basedb.util.jep.Jep

Convert a JEP expression to a Query API Expression.

jepToRestriction(JEP) - Static method in class net.sf.basedb.util.jep.Jep

Convert a JEP expression to a Query API Restriction.

job - Variable in class net.sf.basedb.clients.jobagent.JobRunner

job - Variable in class net.sf.basedb.core.data.ArrayDesignData

job - Variable in class net.sf.basedb.core.data.ChangeHistoryData

job - Variable in class net.sf.basedb.core.data.DerivedBioAssayData

job - Variable in class net.sf.basedb.core.data.ExtraValueData

job - Variable in class net.sf.basedb.core.data.MessageData

job - Variable in class net.sf.basedb.core.data.RawBioAssayData

job - Variable in class net.sf.basedb.core.data.TransformationData

job - Variable in class net.sf.basedb.core.Job.ProgressReporterImpl

job - Variable in class net.sf.basedb.core.ParameterValuesImpl

job - Variable in class net.sf.basedb.core.plugin.AbstractPlugin

job - Variable in class net.sf.basedb.core.plugin.ParameterValuesWrapper

job - Variable in class net.sf.basedb.core.PluginRequest

job - Variable in class net.sf.basedb.core.Transformation

Job - Class in net.sf.basedb.core

This class represents the execution of a job.

Job(JobData) - Constructor for class net.sf.basedb.core.Job

JOB - Enum constant in enum class net.sf.basedb.core.Item

The item is a Job

Job.ExecutionTime - Enum Class in net.sf.basedb.core

A rough estimate of the execution time of a job.

Job.JobSignalTransporter - Class in net.sf.basedb.core

Wrapper for the signal transporter that intercepts the ABORT signal and changes the job's status to ABORTING.

Job.ProgressReporterImpl - Class in net.sf.basedb.core

Implements the ProgressReporter interface and stores the percentage completed for the current job.

Job.SignalKeyring - Class in net.sf.basedb.core

Our own keyring containing the permissions signal handlers may need to update job status, eq.

Job.Status - Enum Class in net.sf.basedb.core

The status of a job.

Job.Type - Enum Class in net.sf.basedb.core

The type of job.

jobAgent - Variable in class net.sf.basedb.core.data.JobAgentSettingsData

JobAgent - Class in net.sf.basedb.core

This class represents a job agent, which is a program running in another virtual machine on the same or a different server.

JobAgent(JobAgentData) - Constructor for class net.sf.basedb.core.JobAgent

JOBAGENT - Enum constant in enum class net.sf.basedb.core.Item

The item is a JobAgent

JOBAGENT - Static variable in class net.sf.basedb.core.Role

The id for the Role item representing job agents.

JobAgentConnection - Class in net.sf.basedb.util.jobagent

This class is used by client applications to communicate with job agents.

JobAgentConnection(int, int) - Constructor for class net.sf.basedb.util.jobagent.JobAgentConnection

Create a connection to the local job agent running on the specified port.

JobAgentConnection(String, int, int) - Constructor for class net.sf.basedb.util.jobagent.JobAgentConnection

Create a connection to the job agent running on the specified server and listening on the specified port.

JobAgentData - Class in net.sf.basedb.core.data

This class holds information about a job agent.

JobAgentData() - Constructor for class net.sf.basedb.core.data.JobAgentData

jobAgentId - Variable in class net.sf.basedb.core.data.JobData

JobAgentInfo - Class in net.sf.basedb.util.jobagent

This class can hold information about the status of a job agent.

JobAgentInfo() - Constructor for class net.sf.basedb.util.jobagent.JobAgentInfo

Create a new info object and set all values to null.

JobAgentInfo(Boolean, Integer, Long, Long, Set<JobInfo>) - Constructor for class net.sf.basedb.util.jobagent.JobAgentInfo

Create a new info object.

JobAgentInfo(String) - Constructor for class net.sf.basedb.util.jobagent.JobAgentInfo

Create a new info object and parse the answer from a JobAgentConnection to get the values.

JobAgentServerConnection - Class in net.sf.basedb.util.jobagent

This class is used by job agents to listen for incoming requests from client applications.

JobAgentServerConnection(int, RequestHandler, Logger) - Constructor for class net.sf.basedb.util.jobagent.JobAgentServerConnection

Create a new server connection.

JobAgentServerConnection.ListenerThread - Class in net.sf.basedb.util.jobagent

This class is used for listening to the specified socket for incoming connections.

JobAgentServerConnection.RequestHandlerThread - Class in net.sf.basedb.util.jobagent

This class is used for forwarding requests to a RequestHandler.

jobAgentSettings - Variable in class net.sf.basedb.core.data.PluginDefinitionData

JobAgentSettings - Class in net.sf.basedb.core

This class contains a job agent's settings for a specific plugin.

JobAgentSettings(JobAgentSettingsData) - Constructor for class net.sf.basedb.core.JobAgentSettings

JOBAGENTSETTINGS - Enum constant in enum class net.sf.basedb.core.Item

The item is a JobAgentSettings

JobAgentSettingsData - Class in net.sf.basedb.core.data

This class holds information about plugin settings for a particular job agent.

JobAgentSettingsData() - Constructor for class net.sf.basedb.core.data.JobAgentSettingsData

jobData - Variable in class net.sf.basedb.core.InternalJobQueue.JobRunner

JobData - Class in net.sf.basedb.core.data

This class holds information about a job.

JobData() - Constructor for class net.sf.basedb.core.data.JobData

jobDone(InternalJobQueue.JobRunner) - Method in class net.sf.basedb.core.InternalJobQueue

Called from a InternalJobQueue.JobRunner when it has finished executing the job.

jobDone(Job, Slot) - Method in class net.sf.basedb.clients.jobagent.Agent

Used by JobRunner to tell that a job has finished executing and that the used slot should be released.

jobExecutor - Variable in class net.sf.basedb.clients.jobagent.Agent

jobExecutor - Variable in class net.sf.basedb.clients.jobagent.JobRunner

JobExecutor - Interface in net.sf.basedb.clients.jobagent

This interface must be implemented by all classes that want's to act as a job executor.

jobId - Variable in class net.sf.basedb.core.data.ChangeHistoryData

jobId - Variable in class net.sf.basedb.core.InternalJobQueue.JobRunner

jobId - Variable in class net.sf.basedb.core.Job.ProgressReporterImpl

jobId - Variable in class net.sf.basedb.core.log.TransactionDetails

jobId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba

jobId - Variable in class net.sf.basedb.core.SessionControl

jobId - Variable in class net.sf.basedb.util.jobagent.JobInfo

JobInfo - Class in net.sf.basedb.util.jobagent

Hold information about a job that is running on a job agent.

JobInfo(int, Map<String, List<String>>) - Constructor for class net.sf.basedb.util.jobagent.JobInfo

Create a new JobInfo object using information from the answer to a JobAgentConnection request.

JobInfo(Job, Job.ExecutionTime) - Constructor for class net.sf.basedb.util.jobagent.JobInfo

Create a new JobInfo object.

jobName - Variable in class net.sf.basedb.core.log.TransactionDetails

jobName - Variable in class net.sf.basedb.core.SessionControl

JobParameter(String...) - Constructor for class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter

JobParameter(Element) - Constructor for class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter

jobParameters - Variable in class net.sf.basedb.core.PluginRequest

jobParameters - Variable in class net.sf.basedb.plugins.Base1PluginExecuter

This list holds the job parameters derived from the configuration file.

jobParametersParameter - Variable in class net.sf.basedb.plugins.Base1PluginExecuter

This parameter describes the job parameters that the base1 plugin needs.

jobPermissions - Variable in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring

jobQuery - Variable in class net.sf.basedb.clients.jobagent.JobQueueChecker

Cached query for waiting jobs.

jobQueueChecker - Variable in class net.sf.basedb.clients.jobagent.Agent

JobQueueChecker - Class in net.sf.basedb.clients.jobagent

This class is given the responsibility to check the job queue for jobs that are awaiting execution.

JobQueueChecker(Agent) - Constructor for class net.sf.basedb.clients.jobagent.JobQueueChecker

JobQueueKeyring() - Constructor for class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring

JobRunner - Class in net.sf.basedb.clients.jobagent

A runnable class that makes it possible to execute each job in it's own thread.

JobRunner(Agent, Job, JobAgentSettings, JobExecutor) - Constructor for class net.sf.basedb.clients.jobagent.JobRunner

Create a new job execution thread.

JobRunner(JobData, Job.ExecutionTime) - Constructor for class net.sf.basedb.core.InternalJobQueue.JobRunner

jobs - Variable in class net.sf.basedb.core.data.ExperimentData

jobs - Variable in class net.sf.basedb.util.jobagent.JobAgentInfo

JobSignalTransporter(SignalTransporter) - Constructor for class net.sf.basedb.core.Job.JobSignalTransporter

join(Collection<?>, String, boolean) - Static method in class net.sf.basedb.core.StringUtil

Join a collection of values to a string, using the specified delimiator.

join(Join) - Method in class net.sf.basedb.core.AbstractQuery

join(Join) - Method in interface net.sf.basedb.core.query.Query

Add a join query element to the join list.

Join - Interface in net.sf.basedb.core.query

A join query element.

JOIN - Enum constant in enum class net.sf.basedb.core.query.QuerySection

joinAlias - Variable in class net.sf.basedb.core.query.ReporterListExpression

joinedAlias - Variable in class net.sf.basedb.core.query.AnnotationJoin

joinedAlias - Variable in class net.sf.basedb.core.query.HqlInnerJoin

joinedAlias - Variable in class net.sf.basedb.core.query.HqlLeftJoin

joinedAlias - Variable in class net.sf.basedb.core.query.HqlRightJoin

joinedItems - Variable in class net.sf.basedb.core.DynamicPositionQuery

joinedItems - Variable in class net.sf.basedb.core.DynamicRawDataQuery

joinedItems - Variable in class net.sf.basedb.core.DynamicReporterQuery

joinedItems - Variable in class net.sf.basedb.core.DynamicSpotQuery

joinExpression - Variable in enum class net.sf.basedb.core.query.JoinType

joinExtraValue(ExtraValue, JoinType) - Method in class net.sf.basedb.core.DynamicPositionQuery

Join extra values in the query.

joinExtraValue(ExtraValue, JoinType) - Method in class net.sf.basedb.core.DynamicSpotQuery

Join extra values in the query.

joinIfNeeded(DynamicPositionQuery, ExtraValueExpression) - Method in class net.sf.basedb.core.DynamicPositionQueryJoiners.ExtraValueJoiner

joinIfNeeded(DynamicPositionQuery, ReporterListExpression) - Method in class net.sf.basedb.core.DynamicPositionQueryJoiners.ReporterListJoiner

joinIfNeeded(DynamicPositionQuery, ReporterPropertyExpression) - Method in class net.sf.basedb.core.DynamicPositionQueryJoiners.ReporterJoiner

joinIfNeeded(DynamicRawDataQuery, ReporterListExpression) - Method in class net.sf.basedb.core.DynamicRawDataQuery.ReporterListJoiner

joinIfNeeded(DynamicRawDataQuery, RawBioAssayPropertyExpression) - Method in class net.sf.basedb.core.DynamicRawDataQuery.RawBioAssayJoiner

joinIfNeeded(DynamicRawDataQuery, ReporterPropertyExpression) - Method in class net.sf.basedb.core.DynamicRawDataQuery.ReporterJoiner

joinIfNeeded(DynamicReporterQuery, ReporterListExpression) - Method in class net.sf.basedb.core.DynamicReporterQuery.ReporterListJoiner

joinIfNeeded(DynamicReporterQuery, ReporterPropertyExpression) - Method in class net.sf.basedb.core.DynamicReporterQuery.MasterReporterJoiner

joinIfNeeded(DynamicSpotQuery, ExtraValueExpression) - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.ExtraValueJoiner

joinIfNeeded(DynamicSpotQuery, ReporterListExpression) - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.ReporterListJoiner

joinIfNeeded(DynamicSpotQuery, RawDataPropertyExpression) - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.RawDataJoiner

joinIfNeeded(DynamicSpotQuery, ReporterPropertyExpression) - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.ReporterJoiner

joinIfNeeded(HqlQuery, AnnotationExpression) - Method in class net.sf.basedb.core.HqlQueryJoiners.AnnotationJoiner

joinIfNeeded(HqlQuery, ReporterListExpression) - Method in class net.sf.basedb.core.HqlQueryJoiners.ReporterListJoiner

joinIfNeeded(Q, E) - Method in interface net.sf.basedb.core.query.AutoJoiner

Automatically join the tables that is is needed by the query element unless they are already joined.

joinMasterReporters(JoinType) - Method in class net.sf.basedb.core.DynamicReporterQuery

Join the master reporter table into this query.

joinPermanent(Join) - Method in class net.sf.basedb.core.AbstractQuery

joinPermanent(Join) - Method in interface net.sf.basedb.core.query.Query

Permanently add a join query element to the join list.

joinProperty - Variable in class net.sf.basedb.core.query.ReporterListExpression

joinRawBioAssay(JoinType) - Method in class net.sf.basedb.core.DynamicRawDataQuery

Join information about raw bioassays in the query.

joinRawData(JoinType) - Method in class net.sf.basedb.core.DynamicSpotQuery

Join information about raw data in the query.

joinReporterList(ReporterList, JoinType) - Method in class net.sf.basedb.core.DynamicPositionQuery

Makes a join with a ReporterList

joinReporterList(ReporterList, JoinType) - Method in class net.sf.basedb.core.DynamicRawDataQuery

Makes a join with a ReporterList

joinReporterList(ReporterList, JoinType) - Method in class net.sf.basedb.core.DynamicReporterQuery

Makes a join with a ReporterList

joinReporterList(ReporterList, JoinType) - Method in class net.sf.basedb.core.DynamicSpotQuery

Makes a join with a ReporterList

joinReporters(JoinType) - Method in class net.sf.basedb.core.DynamicPositionQuery

Join information about reporters in the query.

joinReporters(JoinType) - Method in class net.sf.basedb.core.DynamicRawDataQuery

Join information about reporters in the query.

joinReporters(JoinType) - Method in class net.sf.basedb.core.DynamicSpotQuery

Join information about reporters in the query.

joinReporters(JoinType, boolean) - Method in class net.sf.basedb.core.DynamicPositionQuery

Join information about reporters in the query.

joinReporters(JoinType, boolean) - Method in class net.sf.basedb.core.DynamicSpotQuery

Join information about reporters in the query.

joins - Variable in class net.sf.basedb.core.AbstractQuery

List of joins added to the query.

joinTransaction() - Method in class net.sf.basedb.core.hibernate.SessionWrapper

joinType - Variable in class net.sf.basedb.core.DynamicJoin

joinType - Variable in class net.sf.basedb.core.DynamicPositionQueryJoiners.ExtraValueJoiner

joinType - Variable in class net.sf.basedb.core.DynamicPositionQueryJoiners.ReporterJoiner

joinType - Variable in class net.sf.basedb.core.DynamicPositionQueryJoiners.ReporterListJoiner

joinType - Variable in class net.sf.basedb.core.DynamicRawDataQuery.RawBioAssayJoiner

joinType - Variable in class net.sf.basedb.core.DynamicRawDataQuery.ReporterJoiner

joinType - Variable in class net.sf.basedb.core.DynamicRawDataQuery.ReporterListJoiner

joinType - Variable in class net.sf.basedb.core.DynamicReporterQuery.MasterReporterJoiner

joinType - Variable in class net.sf.basedb.core.DynamicReporterQuery.ReporterListJoiner

joinType - Variable in class net.sf.basedb.core.DynamicSpotQueryJoiners.ExtraValueJoiner

joinType - Variable in class net.sf.basedb.core.DynamicSpotQueryJoiners.RawDataJoiner

joinType - Variable in class net.sf.basedb.core.DynamicSpotQueryJoiners.ReporterJoiner

joinType - Variable in class net.sf.basedb.core.DynamicSpotQueryJoiners.ReporterListJoiner

joinType - Variable in class net.sf.basedb.core.ExtraValueJoin

joinType - Variable in class net.sf.basedb.core.HqlQueryJoiners.AnnotationJoiner

joinType - Variable in class net.sf.basedb.core.HqlQueryJoiners.ReporterListJoiner

joinType - Variable in class net.sf.basedb.core.query.AnnotationJoin

joinType - Variable in class net.sf.basedb.core.RealJoin

joinType - Variable in class net.sf.basedb.core.ReporterListJoin

JoinType - Enum Class in net.sf.basedb.core.query

An enumeration used to specify the type of join.

JoinType(String) - Constructor for enum class net.sf.basedb.core.query.JoinType

jsonColumnDefs - Variable in class net.sf.basedb.clients.web.taglib.table.Table

JsonConverter<T> - Interface in net.sf.basedb.util.json

Implementations should convert a given object to an object that can be serialized into a JSON string.

JsonUtil - Class in net.sf.basedb.util.json

Utility functions for working with JSON data.

JsonUtil() - Constructor for class net.sf.basedb.util.json.JsonUtil

jspContext - Variable in class net.sf.basedb.clients.web.extensions.edit.AbstractOnSaveAction

jspContext - Variable in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerUtil

jspContext - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper

jspContext - Variable in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory.Section

jspContext - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef

JspContext - Class in net.sf.basedb.clients.web.extensions

Context object for the web application.

JspContext(SessionControl, DbControl, ItemContext, PageContext, GuiContext, Object) - Constructor for class net.sf.basedb.clients.web.extensions.JspContext

jspPage - Variable in class net.sf.basedb.core.RequestInformation

K

kB - Static variable in class net.sf.basedb.util.Values

keepFirstWord - Static variable in class net.sf.basedb.clients.web.taglib.Button

keepSkippedLines - Variable in class net.sf.basedb.util.parser.FlatFileParser

If unknown or ignored lines should be kept.

key - Variable in class net.sf.basedb.util.bfs.MetadataModel.SectionEntry

key - Variable in class net.sf.basedb.util.Enumeration.Entry

key - Variable in class net.sf.basedb.util.fuzzy.StringMatcher.FuzzyMatch

key - Variable in class net.sf.basedb.util.gtf.GtfInputStream.Attribute

key - Variable in class net.sf.basedb.util.overview.validator.ExtensionNodeValidator

key - Variable in class net.sf.basedb.util.StaticCache.LockSafeInputStream

key - Variable in class net.sf.basedb.util.StaticCache.LockSafeOutputStream

key(byte[]) - Method in class net.sf.basedb.util.bcrypt.BCrypt

Key the Blowfish cipher

Key - Class in net.sf.basedb.core

This is the base class for keys.

Key(KeyData) - Constructor for class net.sf.basedb.core.Key

KeyData - Class in net.sf.basedb.core.data

This abstract class is the base class for the key classes which holds access privileges for users, groups, projects and roles.

KeyData() - Constructor for class net.sf.basedb.core.data.KeyData

keyId - Variable in class net.sf.basedb.core.data.keyring.KeyPermission

keyId - Variable in class net.sf.basedb.core.data.keyring.PluginKeys

KeyPermission - Class in net.sf.basedb.core.data.keyring

Class for holding a keyId and a permission value.

KeyPermission() - Constructor for class net.sf.basedb.core.data.keyring.KeyPermission

Create a new KeyPermission object.

keyRef - Variable in class net.sf.basedb.util.StaticCache.LockEntry

keyring - Variable in class net.sf.basedb.core.SessionControl.LoginInfo

The Keyring of the logged in user.

Keyring - Class in net.sf.basedb.core

Objects of this class holds information about a user's access permissions, group and role membership.

Keyring(int) - Constructor for class net.sf.basedb.core.Keyring

Create a new Keyring object.

Keyring(Keyring, int, boolean) - Constructor for class net.sf.basedb.core.Keyring

Keyring.ReloadTask - Class in net.sf.basedb.core

keys - Variable in class net.sf.basedb.core.data.RoleData

keyStore - Variable in class net.sf.basedb.util.ssl.StaticKeyManager

kit - Variable in class net.sf.basedb.core.data.BioMaterialEventData

kit - Variable in class net.sf.basedb.core.data.BioPlateEventData

kit - Variable in class net.sf.basedb.core.data.DerivedBioAssayData

Kit - Class in net.sf.basedb.core

This class is used to represent a kit of reagents and other stuff used in the lab process.

Kit(KitData) - Constructor for class net.sf.basedb.core.Kit

Creates a new kit item.

KIT - Enum constant in enum class net.sf.basedb.core.Item

The item is a Kit.

KIT_USED_AFTER_EXPIRATIONDATE - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if a kit has been used after it's exiration date.

kitColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

KitData - Class in net.sf.basedb.core.data

This class holds information about a kit.

KitData() - Constructor for class net.sf.basedb.core.data.KitData

KitImporter - Class in net.sf.basedb.plugins.batchimport

Plug-in for importing kit items in a batch.

KitImporter() - Constructor for class net.sf.basedb.plugins.batchimport.KitImporter

KitLoader - Class in net.sf.basedb.util.overview.loader

Node loader implementation for kits.

KitLoader() - Constructor for class net.sf.basedb.util.overview.loader.KitLoader

kitMapper - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

kitMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter

kitMapper - Variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter

kitMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter

kitQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

KitValidator - Class in net.sf.basedb.util.overview.validator

Validator implementation for kits.

KitValidator() - Constructor for class net.sf.basedb.util.overview.validator.KitValidator

knownFiles - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

Files that are known to exists in the working directory.

L

label - Variable in class net.sf.basedb.core.data.ParameterValueData

label - Variable in class net.sf.basedb.core.ParameterInfo

label - Variable in class net.sf.basedb.core.PluginParameter

A short label used by the client application as in the GUI.

Label - Class in net.sf.basedb.clients.web.taglib.table

This tag creates a label on a toolbar.

Label() - Constructor for class net.sf.basedb.clients.web.taglib.table.Label

LABEL - Static variable in class net.sf.basedb.core.Tag

The ID for the LABEL tag type.

LABELED - Static variable in class net.sf.basedb.core.Extract

The id for the ExtractType item representing a labeled extract.

labeledExtractQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

LABELING - Static variable in class net.sf.basedb.core.Kit

The ID for the labeling kit type, for example a kit used when creating a labeled extract from an Extract.

LABELING - Static variable in class net.sf.basedb.core.Protocol

The ID for the labeling protocol type, for example a protocol used when creating a labeled extract from an Extract.

LAST_SOURCE - Static variable in class net.sf.basedb.core.ClonableProperty

The property name of the "static" property ReporterData.getLastSource()

LAST_UPDATE - Static variable in class net.sf.basedb.core.ClonableProperty

The property name of the "static" property ReporterData.getLastUpdate()

lastAccess - Variable in class net.sf.basedb.core.SessionControl

The time of the last access to this object.

lastColumn - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo

lastCountDc - Variable in class net.sf.basedb.core.AbstractHqlQuery

The most recent DbControl used to build/execute the count query.

lastCountQuery - Variable in class net.sf.basedb.core.AbstractHqlQuery

The most recent count query.

lastError - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtension

lastError - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint

lastErrorAction - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtension

lastErrorAction - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint

lastIdDc - Variable in class net.sf.basedb.core.AbstractHqlQuery

The most recent DbControl used to build/execute the ID query.

lastIdentifier - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

lastIdQuery - Variable in class net.sf.basedb.core.AbstractHqlQuery

The most recent id query.

lastIndexOf(Object) - Method in class net.sf.basedb.core.ItemResultList

lastItem - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

lastLength - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile

lastMainDc - Variable in class net.sf.basedb.core.AbstractHqlQuery

The most recent DbControl used to build/execute the main query.

lastMainQuery - Variable in class net.sf.basedb.core.AbstractHqlQuery

The most recent main query.

lastModified - Variable in class net.sf.basedb.clients.web.extensions.XJspCompiler

lastModified - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile

lastModified - Variable in class net.sf.basedb.util.JarClassLoader.JarInfo

lastModified - Variable in class net.sf.basedb.util.uri.UriMetadata

lastMsg - Variable in class net.sf.basedb.core.Migration.ProgressInputStream

lastName - Variable in class net.sf.basedb.util.extensions.xml.XmlLoader

lastProtocolNode - Variable in class net.sf.basedb.util.overview.validator.ProtocolParameterValidator

lastReset - Static variable in class net.sf.basedb.clients.web.servlet.RssNewsFeed

lastResults - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsManager

lastRow - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo

lastSource - Variable in class net.sf.basedb.core.data.ReporterData

The source of the last update

lastSyncProperties - Variable in class net.sf.basedb.core.data.ItemListSyncFilterData

lastUpdate - Static variable in class net.sf.basedb.clients.web.servlet.RssNewsFeed

lastUpdate - Variable in class net.sf.basedb.core.data.AnnotationData

lastUpdate - Variable in class net.sf.basedb.core.data.FileData

lastUpdate - Variable in class net.sf.basedb.core.data.ReporterData

The last update date.

lastUpdate - Variable in class net.sf.basedb.core.Job.ProgressReporterImpl

lastUpdate - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot

lastUpdated - Variable in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlot

lastUpdated - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo

lastUsed - Variable in class net.sf.basedb.core.data.UserDeviceData

lastValue - Variable in class net.sf.basedb.core.Job.ProgressReporterImpl

latitude - Variable in class net.sf.basedb.util.GeoLocation

LAYER - Static variable in class net.sf.basedb.core.VirtualColumn

This column stores the data cube layer coordinate.

layerNo - Variable in class net.sf.basedb.core.data.DataCubeLayerData

layers - Variable in class net.sf.basedb.core.data.DataCubeData

lazy - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper

LEADING_TRAILING_LINEBREAKS - Static variable in class net.sf.basedb.clients.web.util.HTML

leaveStdinParameter - Variable in class net.sf.basedb.plugins.Base1PluginExecuter

If the plug-in should leave the stdin.txt after execution.

leaveStdoutParameter - Variable in class net.sf.basedb.plugins.Base1PluginExecuter

If the plug-in should leave the stdout.txt after execution.

left - Variable in class net.sf.basedb.core.DynamicJoin

left - Variable in class net.sf.basedb.core.ExtraValueJoin

LEFT - Enum constant in enum class net.sf.basedb.core.query.JoinType

Use a left join, ie. select all rows from the left table and use null if no row is present in the right table.

leftAlias - Variable in class net.sf.basedb.core.ReporterListJoin

leftColumn - Variable in class net.sf.basedb.core.ReporterListJoin

leftColumns - Variable in class net.sf.basedb.core.DynamicJoin

LeftFunction - Class in net.sf.basedb.util.jep

Adds a left(string, index|string) function to Jep.

LeftFunction() - Constructor for class net.sf.basedb.util.jep.LeftFunction

leftJoin(String, String) - Static method in class net.sf.basedb.core.query.Hql

Same as leftJoin(null, propert, joinedAlias, null, false)

leftJoin(String, String, String, Restriction, boolean) - Static method in class net.sf.basedb.core.query.Hql

Create a left join query element.

leftJoin(String, AnnotationType, String) - Static method in class net.sf.basedb.core.query.Annotations

Create a left join between an already joined element of a query and the annotation values for the given annotation type.

leftJoin(AnnotationType, String) - Static method in class net.sf.basedb.core.query.Annotations

Create a left join between the root element of a query and the annotation values for the given annotation type.

leftPad(String, char, int) - Static method in class net.sf.basedb.util.MD5

If the string is shorter than the specified length, it is left padded with the specified character.

length - Variable in class net.sf.basedb.core.data.ReporterClonePropertyData

length - Variable in class net.sf.basedb.core.ExtendedProperty

length - Variable in class net.sf.basedb.util.uri.UriMetadata

LENGTH - Static variable in class net.sf.basedb.core.Quantity

The id for the Quantity object representing length.

lengthOfContextPath - Variable in class net.sf.basedb.clients.web.servlet.ImageRemapFilter

LessConverter - Class in net.sf.basedb.util.jep.convert

Convert the '<' operator to a Query API Restriction.

LessConverter() - Constructor for class net.sf.basedb.util.jep.convert.LessConverter

LessEqualsConverter - Class in net.sf.basedb.util.jep.convert

Convert the '<=' operator to a Query API Restriction.

LessEqualsConverter() - Constructor for class net.sf.basedb.util.jep.convert.LessEqualsConverter

level - Variable in class net.sf.basedb.util.extensions.logging.LogEntry

level - Variable in class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory

Level() - Constructor for enum class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory.Level

LIBRARY - Static variable in class net.sf.basedb.core.Extract

The id for the ExtractType item representing a library.

LIBRARY_PREPARATION - Static variable in class net.sf.basedb.core.Kit

The ID for the library preparation kit type, for example a kit used when creating a library extract from an Extract.

LIBRARY_PREPARATION - Static variable in class net.sf.basedb.core.Protocol

The ID for the library preparation protocol type, for example a protocol used when creating a library extract from an Extract.

like(Expression, Expression) - Static method in class net.sf.basedb.core.query.Restrictions

Check if one expression matches another: e1 LIKE e2

LIKE - Enum constant in enum class net.sf.basedb.core.Operator

like_in(Expression, Expression...) - Static method in class net.sf.basedb.core.query.Restrictions

Check if one expression matches any expressions in an array: (e1 LIKE e2.1) OR (e1 LIKE e2.2) OR ....

LIKE_IN - Enum constant in enum class net.sf.basedb.core.Operator

LikeRestriction - Class in net.sf.basedb.core.query

Check if one expression matches another: e1 LIKE e2

LikeRestriction(Expression, Expression) - Constructor for class net.sf.basedb.core.query.LikeRestriction

limit - Variable in class net.sf.basedb.core.DynamicResultIterator

limit - Variable in class net.sf.basedb.core.signal.ProgressReporterSignalHandler

When the progress has reached this limit signal checking becomes disabled.

line - Variable in class net.sf.basedb.core.MigrateRbaToDba.LineMapping

line - Variable in class net.sf.basedb.util.parser.FlatFileParser.Data

line - Variable in class net.sf.basedb.util.parser.FlatFileParser.Line

line() - Method in class net.sf.basedb.util.parser.FlatFileParser.Data

The entire line as it was read from the input stream.

line() - Method in class net.sf.basedb.util.parser.FlatFileParser.Line

The entire line as it was read from the input stream.

Line(int, String, String, String) - Constructor for class net.sf.basedb.util.parser.FlatFileParser.Line

Create a new header line object.

Line(int, String, String, FlatFileParser.LineType) - Constructor for class net.sf.basedb.util.parser.FlatFileParser.Line

Create a new section line object.

Line(int, String, FlatFileParser.LineType) - Constructor for class net.sf.basedb.util.parser.FlatFileParser.Line

Create a new line object.

LinearScaleFactor(float) - Constructor for class net.sf.basedb.util.InputStreamTracker.LinearScaleFactor

LinearUnitConverter - Class in net.sf.basedb.util.units

A linear unit converter is a converter implementation were all units can be converted to another unit using a multiplication factor and/or an offset.

LinearUnitConverter(double, double) - Constructor for class net.sf.basedb.util.units.LinearUnitConverter

Create a new unit converter.

LinearUnitConverter(double, double, double, double) - Constructor for class net.sf.basedb.util.units.LinearUnitConverter

Create a unit converter that converts between two units that are both related to a third "common" unit by given factors and offsets.

LinearUnitConverter(Unit) - Constructor for class net.sf.basedb.util.units.LinearUnitConverter

Create a new unit converter that converts to/from a given unit.

LinearUnitConverter(Unit, Unit) - Constructor for class net.sf.basedb.util.units.LinearUnitConverter

Create a new unit converter that converts to/from given specific and reference unit.

LINEBREAKS_REGEXP - Static variable in class net.sf.basedb.clients.web.util.HTML

This pattern can be used to find line breaks.

lineCount - Variable in class net.sf.basedb.util.bfs.MetadataWriter

LineMapping(int, String) - Constructor for class net.sf.basedb.core.MigrateRbaToDba.LineMapping

lineNo - Variable in class net.sf.basedb.core.MigrateRbaToDba.LineMapping

lineNo - Variable in class net.sf.basedb.util.parser.FlatFileParser.Data

lineNo - Variable in class net.sf.basedb.util.parser.FlatFileParser.Line

lineNo() - Method in class net.sf.basedb.util.parser.FlatFileParser.Data

The line number of the data in the input stream.

lineNo() - Method in class net.sf.basedb.util.parser.FlatFileParser.Line

The line number of this line in the input stream.

lineNoFunction - Variable in class net.sf.basedb.util.parser.JepMapper

LineNoFunction - Class in net.sf.basedb.util.parser

Adds a lineNo() function to Jep.

LineNoFunction() - Constructor for class net.sf.basedb.util.parser.LineNoFunction

lineNum - Variable in class net.sf.basedb.util.gtf.GtfInputStream

lines - Variable in class net.sf.basedb.core.MigrateRbaToDba.SubtypeMapping

lines - Variable in class net.sf.basedb.util.parser.FlatFileParser

List of lines parsed by the FlatFileParser.parseHeaders() method.

linesToParse - Variable in class net.sf.basedb.util.gtf.GtfValidationAction

linesToParse - Variable in class net.sf.basedb.util.importer.spotdata.SecondPassSectionSpotsParser

lineTester - Variable in class net.sf.basedb.util.charset.CharsetDetector

LineType(String) - Constructor for enum class net.sf.basedb.util.parser.FlatFileParser.LineType

LINK_EMAIL - Static variable in class net.sf.basedb.clients.web.util.HTML

This flag is used in HTML.scanForLinks(String,int) when you want to create links for email addresses.

LINK_URL - Static variable in class net.sf.basedb.clients.web.util.HTML

This flag is used in HTML.scanForLinks(String,int) when you want to create links for URL:s.

linkAnnotations(AnnotationBatcher.UpdateBatcher) - Method in class net.sf.basedb.core.MigrateRbaToDba.Rba

Link the annotation set to the new derived bioassay.

linkAnyToAny(AnnotationBatcher.UpdateBatcher, AnnotationBatcher.UpdateBatcher) - Method in class net.sf.basedb.core.MigrateRbaToDba.Rba

Link any-to-any links with the new derived bioassay.

linkArrayDesign(AnnotationBatcher.InsertBatcher) - Method in class net.sf.basedb.core.MigrateRbaToDba.Rba

linkAttributes(ClientContext) - Method in class net.sf.basedb.util.extensions.ClientContext

Link this context to the other context with respect to attributes.

linkChangeHistory(AnnotationBatcher.UpdateBatcher) - Method in class net.sf.basedb.core.MigrateRbaToDba.Rba

Link change history entries with the new derived bioassay.

linkDescriptionColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

LinkedFileFormatter - Class in net.sf.basedb.clients.web.formatter

Formatter implementation that generates a HTML output linking a file item.

LinkedFileFormatter() - Constructor for class net.sf.basedb.clients.web.formatter.LinkedFileFormatter

LinkedFileFormatter(boolean, boolean) - Constructor for class net.sf.basedb.clients.web.formatter.LinkedFileFormatter

LinkedFileFormatter(FileViewerUtil) - Constructor for class net.sf.basedb.clients.web.formatter.LinkedFileFormatter

LinkedItemFormatter - Class in net.sf.basedb.clients.web.formatter

Formatter implementation that generates a HTML output linking a nameable item.

LinkedItemFormatter() - Constructor for class net.sf.basedb.clients.web.formatter.LinkedItemFormatter

LinkedItemFormatter(boolean) - Constructor for class net.sf.basedb.clients.web.formatter.LinkedItemFormatter

linkedQuery - Variable in class net.sf.basedb.core.query.AnyToAnyRestriction

linkedRestriction - Variable in class net.sf.basedb.core.query.AnyToAnyRestriction

linkedTo - Variable in class net.sf.basedb.core.query.AnyToAnyRestriction

linkers - Variable in class net.sf.basedb.core.ExtendedProperty

linkFiles(AnnotationBatcher.UpdateBatcher, AnnotationBatcher.UpdateBatcher) - Method in class net.sf.basedb.core.MigrateRbaToDba.Rba

Link the file set to the new derived bioassay and update file types on members.

linkItemValues(Connection, Map<Integer, Integer>) - Method in class net.sf.basedb.core.MigrateRbaToDba

Change raw bioassays that have been used as job parameters to the new derived bioassay.

linkName - Variable in class net.sf.basedb.clients.web.extensions.list.AnyLinkColumn

linkName - Variable in class net.sf.basedb.clients.web.plugins.AnyToAnyDataLoader

linkName - Variable in class net.sf.basedb.core.AnyToAny.FastLinkLoader

linkName - Variable in class net.sf.basedb.core.query.AnyToAnyRestriction

linkName - Variable in class net.sf.basedb.util.AnyToAnyLinkStatistics

linkNameColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

linkNameMapper - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

linkParentBioAssays(AnnotationBatcher.UpdateBatcher, AnnotationBatcher.UpdateBatcher) - Method in class net.sf.basedb.core.MigrateRbaToDba.Rba

links - Variable in class net.sf.basedb.core.AnyToAny.FastLinkLoader

links - Variable in class net.sf.basedb.core.data.AnnotatedData

links - Variable in class net.sf.basedb.core.data.BioAssayData

links - Variable in class net.sf.basedb.core.data.BioAssaySetData

links - Variable in class net.sf.basedb.core.data.PluginDefinitionData

links - Variable in class net.sf.basedb.core.data.ProjectData

links - Variable in class net.sf.basedb.core.data.RootRawBioAssayData

links - Variable in class net.sf.basedb.core.data.WellData

linkType - Variable in class net.sf.basedb.clients.web.plugins.AnyToAnyDataLoader

list - Variable in class net.sf.basedb.clients.web.taglib.table.CellValue

list - Variable in class net.sf.basedb.core.ItemList.DelayedAdditionManager

list() - Method in class net.sf.basedb.core.hibernate.QueryWrapper

list(DbControl) - Method in class net.sf.basedb.core.ItemQuery

Execute the query and return the results as a list.

list(DbControl) - Method in class net.sf.basedb.core.SpecialQuery

Get the result of the query as a list.

list(Item) - Static method in class net.sf.basedb.core.plugin.GuiContext

Shortcut to create a list context.

list(Item, String) - Static method in class net.sf.basedb.core.plugin.GuiContext

Shortcut to create a list context with a subcontext.

LIST - Enum constant in enum class net.sf.basedb.core.plugin.GuiContext.Type

LIST - Static variable in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil

LIST_ITEMS - Static variable in class net.sf.basedb.clients.web.extensions.list.ListColumnUtil

An array containing all items that we are registering an extension point for.

Listable - Interface in net.sf.basedb.core

Tagging interface for items that can be put in an ItemList.

listableItems - Static variable in class net.sf.basedb.core.Metadata

ListableUtil - Class in net.sf.basedb.util.listable

Utility class for working with Listable items.

ListableUtil() - Constructor for class net.sf.basedb.util.listable.ListableUtil

ListColumnAction<I,V> - Interface in net.sf.basedb.clients.web.extensions.list

Action that inserts a new column into a table listing.

ListColumnDataLoader<I> - Class in net.sf.basedb.clients.web.extensions.list

Data loader implementation that acts as a proxy to a ListColumnAction object.

ListColumnDataLoader(ListColumnAction<I, ?>) - Constructor for class net.sf.basedb.clients.web.extensions.list.ListColumnDataLoader

ListColumnExportRenderer<I> - Class in net.sf.basedb.clients.web.extensions.list

Renderer implementation that add formatter and data loader implementation for a list column that can be exported.

ListColumnExportRenderer(ItemContext) - Constructor for class net.sf.basedb.clients.web.extensions.list.ListColumnExportRenderer

ListColumnUtil - Class in net.sf.basedb.clients.web.extensions.list

Utility class for list column extension points.

ListColumnUtil() - Constructor for class net.sf.basedb.clients.web.extensions.list.ListColumnUtil

listener - Variable in class net.sf.basedb.core.signal.SocketSignalReceiver

listener - Variable in class net.sf.basedb.util.jobagent.JobAgentServerConnection

ListenerThread(ServerSocketChannel) - Constructor for class net.sf.basedb.core.signal.SocketSignalReceiver.ListenerThread

ListenerThread(ServerSocketChannel, RequestHandler, Logger) - Constructor for class net.sf.basedb.util.jobagent.JobAgentServerConnection.ListenerThread

listenOnSocket() - Method in class net.sf.basedb.clients.jobagent.AgentSignalReceiver

Do not open any socket.

listenOnSocket() - Method in class net.sf.basedb.core.signal.SocketSignalReceiver

Start listening for incoming signals.

listId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Itemlist

listIterator() - Method in class net.sf.basedb.core.ItemResultList

listIterator(int) - Method in class net.sf.basedb.core.ItemResultList

listMemberType - Variable in class net.sf.basedb.core.SyncFilter

listQuery - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemListColumn

listTables(DatabaseMetaData, String, String) - Static method in class net.sf.basedb.core.dbengine.TableInfo

List all tables that are present in the given catalog and/or schema.

listToMap(List<? extends SettingData>) - Method in class net.sf.basedb.core.SessionControl

Copy settings from a List to a Map.

ListUtil - Class in net.sf.basedb.util

ListUtil() - Constructor for class net.sf.basedb.util.ListUtil

ln(String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine

Return LN(<value>).

ln(String) - Method in interface net.sf.basedb.core.dbengine.DbEngine

Get the function call that takes the natural logarithm of a value.

ln(String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine

Return LOG(<value>).

ln(Expression) - Static method in class net.sf.basedb.core.query.Expressions

Calculate the natural logarithm of an expression: new expression = ln(e).

LN2 - Static variable in enum class net.sf.basedb.core.IntensityTransform

load(Class<T>, Serializable) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

load(Class<T>, Serializable, LockMode) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

load(Class<T>, Serializable, LockOptions) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

load(Object, Serializable) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

load(String, int) - Method in class net.sf.basedb.util.StaticCache

Read a serializable object from the cache.

load(String, Serializable) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

load(String, Serializable, LockMode) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

load(String, Serializable, LockOptions) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

load(String, ClassLoader, int) - Method in class net.sf.basedb.util.StaticCache

load(Collection<? extends Annotatable>) - Method in class net.sf.basedb.core.FastAnnotationLoader

Load the annotation values for all items in the given collection.

load(Iterator<? extends Annotatable>) - Method in class net.sf.basedb.core.FastAnnotationLoader

Load the annotation values for all items returned by the given iterator.

load(ItemQuery<? extends Annotatable>) - Method in class net.sf.basedb.core.FastAnnotationLoader

Load the annotation values for all items returned by the query.

loadAbout(Element) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader

Load information in an <about> tag.

loadAnnotationInfo - Variable in class net.sf.basedb.core.AnnotationBatcher

loadAnnotationValues - Variable in class net.sf.basedb.core.AnnotationBatcher

loadAttributes(ItemContext, String) - Method in class net.sf.basedb.util.extensions.ClientContext

Load attributes to this context from the given ItemContext instance.

loadCdfFile(File) - Method in class net.sf.basedb.util.affymetrix.CdfValidator

Load a CDF file using the Affymetric Fusion SDK.

loadCelFile(File) - Method in class net.sf.basedb.util.affymetrix.CelValidator

Load a CEL file using the Affymetric Fusion SDK.

loadChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AbstractNodeLoader

Load childs nodes.

loadChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AutoChildNodeLoader

Call the same method on the 'parent' node loader.

loadChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioWellLoader

Delegate loading of child nodes to the actual item loader that this node is representing.

loadChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtensionChildNodeLoader

Call the same method on the 'parent' node loader.

loadChildNodes(DbControl, OverviewContext, Node) - Method in interface net.sf.basedb.util.overview.loader.NodeLoader

Load child nodes of the current node unless they have been loaded already.

loadChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.NullNodeLoader

loadChildNodesOfFolderNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AbstractNodeLoader

Iterates the children of a folder-type node and loads the children for each one of them.

loadChildNodesOfItemNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AbstractNodeLoader

Loads child nodes of an item-type node.

loadClass(String, boolean) - Method in class net.sf.basedb.util.JarClassLoader

loadClassData(File, String) - Method in class net.sf.basedb.util.JarClassLoader

Load the byte[] of the given class.

loadClasses(Set<String>, Document, String) - Static method in class net.sf.basedb.core.ExtendedProperties

Load the classes and put their names in the ExtendedProperties.classes variable.

loadClassInternal(ClassLoader, String) - Method in class net.sf.basedb.util.JarClassLoader

loadClientDefaultSettings(Session, int) - Method in class net.sf.basedb.core.SessionControl

Load client applications default settings.

loadContext(int) - Method in class net.sf.basedb.core.SessionControl

Load a context and make it the current context.

loadContext(int, boolean) - Method in class net.sf.basedb.core.SessionControl

Load a context and make it the current context, optionally copying temporary filters and objects from the current context to the loaded context.

loadContext(SessionControl, int, ItemContext) - Static method in class net.sf.basedb.clients.web.Base

loadContextInternal(int) - Method in class net.sf.basedb.core.SessionControl

Load a context with the specified ID.

loadContextInternal(Item, String, String) - Method in class net.sf.basedb.core.SessionControl

Load a named context.

loadData(Class<T>, Query<T>, StatelessSession, SessionControl) - Static method in class net.sf.basedb.core.QueryExecutor

Executes a Hibernate query on a stateless session.

loadData(Query<T>) - Static method in class net.sf.basedb.core.HibernateUtil

Load a data item from the database using a query.

loadData(Session, Class<T>, int) - Static method in class net.sf.basedb.core.HibernateUtil

Load a data item from the database when you know the id.

loadData(Session, Class<T>, String, int) - Static method in class net.sf.basedb.core.HibernateUtil

Load a data item from the database when you know the id.

loadData(StatelessSession, Class<T>, int) - Static method in class net.sf.basedb.core.HibernateUtil

Load a data item from the database using a statless session when you know the id.

loadData(StatelessSession, Class<T>, String, int) - Static method in class net.sf.basedb.core.HibernateUtil

Load a data item from the database using a statless session when you know the id.

loadDevice(Session, LoginRequest, AuthenticatedUser) - Method in class net.sf.basedb.core.SessionControl

Verify the device the user is using.

loadDiskUsage(Query<Object[]>) - Method in class net.sf.basedb.core.DiskUsageStatistics.Summary

loadDocument(InputStream, String) - Method in class net.sf.basedb.clients.web.extensions.ServletLoader

Load and validate the XML file.

loadDocument(InputStream, String) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader

Load and validate the XML file.

loader - Variable in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor

loader - Variable in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor

loader - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredEventHandler

loader - Variable in class net.sf.basedb.util.JarClassLoader.JarClassLoaderProxy

loaders - Variable in class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory

loadExtendedPropertiesFile() - Static method in class net.sf.basedb.core.ExtendedProperties

Load and parse the file with predefined queries.

loadExtensionPoints(Document, ClassLoader, About) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader

Create extension points from an XML document.

loadExtensions(Document, ClassLoader, About) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader

Create extensions from an XML document.

loadExtracts() - Method in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper

Load extracts in parent chain.

loadFiles(DbControl, Collection<Nameable>, Directory) - Method in class net.sf.basedb.plugins.PackedFileExporter

Load files and subdirectories in the given directory.

loadFilesAndDirectories(DbControl, Collection<Nameable>, Collection<Integer>, Collection<Integer>, boolean) - Method in class net.sf.basedb.plugins.PackedFileExporter

Load specified files and directories and put them in loadedFiles.

loadFilterTemplates(String) - Method in class net.sf.basedb.core.HibernateUtil.FilterConfigurator

loadForward - Variable in enum class net.sf.basedb.util.overview.node.ChildNodeDirection

loadForward() - Method in enum class net.sf.basedb.util.overview.node.ChildNodeDirection

loadForwardChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AbstractNodeLoader

Load forward-loading child nodes.

loadForwardChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArrayBatchLoader

Loads the array slide nodes that is related to the given batch node.

loadForwardChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArrayDesignLoader

Loads the array batch nodes that has been created with the given design node.

loadForwardChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArraySlideLoader

Loads the physical bioassay node that is related to the given array slide node.

loadForwardChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioPlateEventLoader

Loads the bioplates that are part of the event.

loadForwardChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioPlateLoader

Loads the non-empty biowells on the bioplate.

loadForwardChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioSourceLoader

Loads the sample nodes that has been created from the given biosource node.

loadForwardChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader

Loads all child derived bioassay and raw bioassay nodes.

loadForwardChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader

Loads the child extracts and physical bioassays that has been created from this extract.

loadForwardChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ItemListLoader

Loads the list members.

loadForwardChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.PhysicalBioAssayLoader

Load forward-loading child nodes: Derived bioassay sets (root): DerivedBioAssayLoader.createForwardNode(DbControl, OverviewContext, Node) Array slide in reverse direction (if the parent node is an extract): ArraySlideLoader.createReverseNode(DbControl, OverviewContext, Node) Extracts in reverse direction (if the parent node is the array slide): ExtractLoader.createReverseNode(DbControl, OverviewContext, Node)

loadForwardChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.RawBioAssayLoader

Loads all experiment nodes where the given raw bioassay is used.

loadForwardChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.SampleLoader

Loads the pooled samples and extracts that has been created from this sample.

loadFrom(InputStream, String) - Method in class net.sf.basedb.core.Presets

Load presets from a stream.

loadFrom(String) - Method in class net.sf.basedb.core.Presets

Load presets from an XML string.

loadFromPreset(Presets.Preset, boolean) - Method in class net.sf.basedb.util.overview.ValidationOptions

Load validation options from a Presets.Preset.

loadGlobalAbout(Document) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader

Load the global about tag from the document.

loadGroups(Session) - Method in class net.sf.basedb.core.Keyring

Loads group membership for the user and put that information in the Keyring.groups and Keyring.groupsWithNonHiddenMembers variables.

loadIdToNameMap(Session, String) - Static method in class net.sf.basedb.core.Update

loadInherited - Variable in class net.sf.basedb.clients.web.plugins.ExportedProperty

loadIntensityFormulas(Element, int, String) - Static method in class net.sf.basedb.core.RawDataTypes

Load the intensity formulas for the specified raw data type node and return a list of IntensityFormula objects.

loadInterfaceInformation(String, String) - Method in class net.sf.basedb.core.PluginType

loadItem(I) - Method in class net.sf.basedb.core.DbControl

Load an item from the database.

loadItem(Class<I>, int) - Method in class net.sf.basedb.core.DbControl

Load an item from the database when you now the id.

loadItemByDataClass(Class<I>, Class<D>, int) - Method in class net.sf.basedb.core.DbControl

Load an item from the database when you know the id.

loadItemId(Session, Item, int) - Static method in class net.sf.basedb.core.AnnotationSet

Load the id of the item that this annotation set belongs to.

loadItemKeys(Session) - Method in class net.sf.basedb.core.Keyring

Load all ItemKey:s for the logged in user and put the result in Keyring.itemPermissions

loadIterator(Query<T>, boolean, SessionControl) - Static method in class net.sf.basedb.core.HibernateUtil

Scroll through the result of a query using an iterator.

loadIterator(Query<T>, StatelessSession, SessionControl) - Static method in class net.sf.basedb.core.QueryExecutor

Executes a Hibernate query that returns an iterator on a stateless session.

loadJarFile(File, boolean) - Method in class net.sf.basedb.util.JarClassLoader

Open the specified JAR file, list all entries and put them in the JarClassLoader.classPath mapping.

loadJsonForBatchInherit(DbControl, AnnotationType) - Static method in class net.sf.basedb.clients.web.AnnotationUtil

Load information about categories and subtypes of an annotation type that are useful for deciding about inheriting annotations from parent items, The result is returned as a JSON object intended to be used by the "Batch inherit annotations" feature in the web interface.

loadLastValidatedFile(ClassLoader, boolean) - Method in class net.sf.basedb.clients.web.extensions.ServletLoader

Continue loading servlet definitions from the last validated XML file.

loadLastValidatedFile(ClassLoader, boolean) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader

Continue loading extensions from the last validated XML file.

loadList(Query<T>, SessionControl) - Static method in class net.sf.basedb.core.HibernateUtil

Load a List of items from the database using a query.

loadMaxProjectPermission(Session, ProjectData) - Method in class net.sf.basedb.core.Keyring

Find out the logged in user's maximum permission to the active project and put the result in Keyring.maxProjectPermission.

loadMemberNodes(BasicItemNodeLoader<T>, DbControl, OverviewContext, Node) - Static method in class net.sf.basedb.util.overview.loader.ItemListLoader

Utiltity method to be used by other loaders to load members of an item list.

loadMinimalDirectoryTree(DbControl, Collection<Include>, Directory...) - Static method in class net.sf.basedb.util.FileUtil

Load a minimal directory tree that includes at least all the specified directories and their parent directories all the way up to the root or as far as the logged in user has read permission.

loadMinimalDirectoryTree(DbControl, Directory...) - Static method in class net.sf.basedb.util.FileUtil

Load a minimal directory tree that includes at least all the specified directories and their parent directories all the way up to the root or as far as the logged in user has read permission.

loadParentReporterPositions(DbControl, BioAssaySet) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo

Load position/reporter mapping from the parent bioassay set.

loadParents - Variable in class net.sf.basedb.util.listable.CollectExtracts.CollectFromDerivedBioAssays

loadPluginDefinitions(Document, ClassLoader, About) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader

Load plug-in information from an XML document.

loadPluginInformation(String, String, boolean) - Method in class net.sf.basedb.core.PluginDefinition

Load a plugin and copy information to the internal data structure.

loadPluginPermissionKeys(Session) - Method in class net.sf.basedb.core.Keyring

Load all PluginKeys:s for the active plugin.

loadPresets(Document) - Method in class net.sf.basedb.core.Presets

Parse an XML Document and load all presets.

loadProjectKeys(Session) - Method in class net.sf.basedb.core.Keyring

Load all ProjectKey:s for the logged in user.

loadProjects(Session) - Method in class net.sf.basedb.core.Keyring

Loads project membership for the user and put that information in the Keyring.projects variable.

loadProperties(Set<String>, Element, String) - Static method in class net.sf.basedb.core.ExtendedProperties

Load the properties for the specified class node and put the list in the ExtendedProperties.allProperties variable.

loadProperties(Element, int, String) - Static method in class net.sf.basedb.core.RawDataTypes

Load the properties for the specified raw data type node and return a list of RawDataProperty objects.

loadProperty - Variable in enum class net.sf.basedb.util.overview.node.ChildNodeDirection

loadProperty() - Method in enum class net.sf.basedb.util.overview.node.ChildNodeDirection

loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AbstractNodeLoader

Load property-type child nodes.

loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AnyToAnyLoader

Loads property nodes of an any-to-any node.

loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArrayBatchLoader

Loads property nodes of an array batch.

loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArrayDesignLoader

Loads property nodes of an array design.

loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArraySlideLoader

Loads property nodes of an array slide.

loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioPlateEventLoader

Loads property nodes of an event.

loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioPlateLoader

Load the freezer node.

loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioSourceLoader

Loads property nodes of an array design.

loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.DataFileLoader

Loads property nodes of files.

loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader

Loads property nodes of a derived bioassay set.

loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExperimentLoader

Load property nodes for an experiment: Experimental factors: ExperimentalFactorLoader.createPropertyNode(DbControl, OverviewContext, Node) Annotations: AnnotationLoader.createPropertyNode(DbControl, OverviewContext, Node)

loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader

Loads property nodes of an extract.

loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.FileLoader

Loads annotations for the given file node.

loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.HardwareLoader

Loads annotations and hardware parameters for the given hardware node.

loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ItemListLoader

Loads property nodes of a item list.

loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.KitLoader

Loads annotations for the given kit node.

loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.PhysicalBioAssayLoader

Loads property nodes of a physical bioassay.

loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ProtocolLoader

Loads annotations and protocol parameters for the given protocol node.

loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.RawBioAssayLoader

Load property nodes for a raw bioassay: Annotations: AnnotationLoader.createPropertyNode(DbControl, OverviewContext, Node) Data files: DataFileLoader.createPropertyNode(DbControl, OverviewContext, Node) Platform: PlatformLoader.createPropertyNode(DbControl, OverviewContext, Node) Protocol: ProtocolLoader.createPropertyNode(DbControl, OverviewContext, Node) Software: SoftwareLoader.createPropertyNode(DbControl, OverviewContext, Node) Array design: ArrayDesignLoader.createPropertyNode(DbControl, OverviewContext, Node)

loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.RootRawBioAssayLoader

Load property nodes for a raw bioassay: Annotations: AnnotationLoader.createPropertyNode(DbControl, OverviewContext, Node) Data files: DataFileLoader.createPropertyNode(DbControl, OverviewContext, Node) Platform: PlatformLoader.createPropertyNode(DbControl, OverviewContext, Node) Protocol: ProtocolLoader.createPropertyNode(DbControl, OverviewContext, Node) Software: SoftwareLoader.createPropertyNode(DbControl, OverviewContext, Node) Array design: ArrayDesignLoader.createPropertyNode(DbControl, OverviewContext, Node)

loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.SampleLoader

Loads property nodes of a sample.

loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.SoftwareLoader

Loads annotations and software parameters for the given software node.

loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.TagLoader

Loads annotations and tag parameters for the given tag node.

loadRawDataTypes(Set<String>, Document, String) - Static method in class net.sf.basedb.core.RawDataTypes

Load the raw data types and put the information in the RawDataTypes.rawDataTypes map.

loadRawDataTypesFile() - Static method in class net.sf.basedb.core.RawDataTypes

Load and parse the file with raw data types.

loadRecent(DbControl, Item, String) - Method in class net.sf.basedb.core.ItemContext

loadRecent(DbControl, Item, String, int) - Method in class net.sf.basedb.core.ItemContext

loadReverse - Variable in enum class net.sf.basedb.util.overview.node.ChildNodeDirection

loadReverse() - Method in enum class net.sf.basedb.util.overview.node.ChildNodeDirection

loadReverseChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AbstractNodeLoader

Load reverse-loading child nodes.

loadReverseChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArrayBatchLoader

Loads the array design node that is the parent of this array batch.

loadReverseChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArraySlideLoader

Loads the array batch node that is the parent of this array slide.

loadReverseChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioSourceLoader

A biosource usually don't have any reverse child nodes.

loadReverseChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader

Loads the parent bioassay or the parent physical bioassay.

loadReverseChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExperimentLoader

Loads the root raw bioassay nodes that are part of this experiment

loadReverseChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader

Load either the parent sample or extract(s) and child extracts+physical bioassays with a subtype that has ItemSubtype.getPushAnnotations() flag set.

loadReverseChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.PhysicalBioAssayLoader

Load reverse child nodes: Extracts: ExtractLoader.createReverseNode(DbControl, OverviewContext, Node) Array slide: ArraySlideLoader.createReverseNode(DbControl, OverviewContext, Node)

loadReverseChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.RawBioAssayLoader

Loads the derived bioassay node that this raw bioassay is created from.

loadReverseChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.RootRawBioAssayLoader

Loads the derived bioassay node that this raw bioassay is created from.

loadReverseChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.SampleLoader

If the sample is a pooled sample, loads the parent samples that it was pooled from.

loadRoleKeys(Session) - Method in class net.sf.basedb.core.Keyring

Load all RoleKey:s for the logged in user and put the result in Keyring.rolePermissions

loadRoles(Session) - Method in class net.sf.basedb.core.Keyring

Loads role membership for the user and put that information in the Keyring.roles variable.

loadServletClass(String, ClassLoader) - Method in class net.sf.basedb.clients.web.extensions.ServletLoader

Load the servlet class.

loadServlets(Document, ClassLoader) - Method in class net.sf.basedb.clients.web.extensions.ServletLoader

Load the servlet definitions from an XML document.

LoadServletsProcessor - Class in net.sf.basedb.clients.web.extensions

Processor implementation that define servlets based on what it can find in the META-INF/servlets.xml file.

LoadServletsProcessor(ServletContext, ProcessResults) - Constructor for class net.sf.basedb.clients.web.extensions.LoadServletsProcessor

loadState(ClassLoader) - Method in class net.sf.basedb.core.Job

Load the saved state from the cache.

loadUserClientSettings(Session, int, int) - Method in class net.sf.basedb.core.SessionControl

Load users client-specific settings.

loadUserDefaultSettings(Session, int) - Method in class net.sf.basedb.core.SessionControl

Load users default settings.

loadUsers(Session) - Method in class net.sf.basedb.core.Keyring

Load all users which are member of at least one group where the logged in user is also a member and put that information in the Keyring.users variable.

loadXmlFile(InputStream, String, ClassLoader, boolean) - Method in class net.sf.basedb.clients.web.extensions.ServletLoader

Load a servlet definition XML file.

loadXmlFile(InputStream, String, ClassLoader, boolean) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader

Load an extensions definition XML file.

loadXmlFile2(InputStream, String) - Static method in class net.sf.basedb.core.PluginConfiguration

Load a configurations xml file from the given stream.

LOCAL_HOST - Static variable in class net.sf.basedb.util.SocketUtil

locale - Static variable in class net.sf.basedb.core.Config

LocalSignalReceiver - Class in net.sf.basedb.core.signal

A signal receiver implementation that can receive signals from the local virtual machine only.

LocalSignalReceiver() - Constructor for class net.sf.basedb.core.signal.LocalSignalReceiver

Create a new local signal receiver.

LocalSignalTransporter - Class in net.sf.basedb.core.signal

A signal transporter implementation that can transport signals within the local virtual machine only.

LocalSignalTransporter() - Constructor for class net.sf.basedb.core.signal.LocalSignalTransporter

Create a new signal transporter instance.

localVersion - Variable in class net.sf.basedb.clients.web.taglib.Head

location - Variable in class net.sf.basedb.core.data.DiskUsageData

location - Variable in class net.sf.basedb.core.data.FileData

location - Variable in class net.sf.basedb.core.data.QuotaIndex

location - Variable in class net.sf.basedb.core.data.SessionData

location - Variable in class net.sf.basedb.core.data.UserDeviceData

location - Variable in class net.sf.basedb.core.SessionControl

Location of the remote IP.

Location - Enum Class in net.sf.basedb.core

This enumeration defines constants that are used to specify different file storage locations.

Location(int, String, boolean, boolean) - Constructor for enum class net.sf.basedb.core.Location

Creates a new location.

locationLat - Variable in class net.sf.basedb.core.data.SessionData

locationLat - Variable in class net.sf.basedb.core.data.UserDeviceData

locationLoaded - Variable in class net.sf.basedb.core.SessionControl

locationLong - Variable in class net.sf.basedb.core.data.SessionData

locationLong - Variable in class net.sf.basedb.core.data.UserDeviceData

locator - Variable in class net.sf.basedb.util.importer.spotdata.BfsImporter

lock - Variable in class net.sf.basedb.util.extensions.logging.ExtensionsLog

lock - Variable in class net.sf.basedb.util.StaticCache.State

lock() - Method in class net.sf.basedb.core.Application.StartupOptions

Lock the options for additional modifications.

lock() - Method in class net.sf.basedb.util.Enumeration

lock(Object, LockModeType) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

lock(Object, LockModeType, Map<String, Object>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

lock(Object, LockMode) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

lock(String, Object, LockMode) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

lockData(Session, BasicData, LockOptions) - Static method in class net.sf.basedb.core.HibernateUtil

Reconnect a disconnected data object to the session, discarding changes that have been made while the object was disconnected.

locked - Variable in class net.sf.basedb.clients.web.taglib.table.Navigator

locked - Variable in class net.sf.basedb.core.Application.StartupOptions

locked - Variable in class net.sf.basedb.core.data.ReporterCloneTemplateData

locked - Variable in class net.sf.basedb.util.Enumeration

LOCKED_AFTER_ADD - Enum constant in enum class net.sf.basedb.core.BioWell.LockMode

It is allowed to add biomaterial once to the well.

LOCKED_AFTER_CREATE - Enum constant in enum class net.sf.basedb.core.BioWell.LockMode

It is allowed to add biomaterial once to the well, but it most be done at the same time the plate is creted.

LOCKED_AFTER_MOVE - Enum constant in enum class net.sf.basedb.core.BioWell.LockMode

It is allowed to add biomaterial once to the well.

lockedColumns - Variable in class net.sf.basedb.util.bfs.DataWriter

LockEntry(ReadWriteLock, String) - Constructor for class net.sf.basedb.util.StaticCache.LockEntry

lockMode - Variable in class net.sf.basedb.core.data.BioPlateTypeData

LockMode(int, String) - Constructor for enum class net.sf.basedb.core.BioWell.LockMode

locks - Variable in class net.sf.basedb.util.StaticCache

LockSafeInputStream(InputStream, StaticCache.LockEntry) - Constructor for class net.sf.basedb.util.StaticCache.LockSafeInputStream

LockSafeOutputStream(OutputStream, StaticCache.LockEntry) - Constructor for class net.sf.basedb.util.StaticCache.LockSafeOutputStream

log - Static variable in class net.sf.basedb.clients.jobagent.Agent

Log job agent events.

log - Static variable in class net.sf.basedb.clients.jobagent.AgentController

Log job agent events.

log - Static variable in class net.sf.basedb.clients.jobagent.executors.DummyJobExecutor

Log job agent events.

log - Static variable in class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor

Log job agent events.

log - Static variable in class net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor

Log job agent events.

log - Static variable in class net.sf.basedb.clients.jobagent.handlers.DefaultRequestHandler

Log job agent events.

log - Static variable in class net.sf.basedb.clients.jobagent.handlers.InfoRequestHandler

log - Static variable in class net.sf.basedb.clients.jobagent.handlers.MultiProtocolRequestHandler

Logger.

log - Static variable in class net.sf.basedb.clients.jobagent.JobQueueChecker

Log job agent events.

log - Static variable in class net.sf.basedb.clients.jobagent.JobRunner

Log job agent events.

log - Static variable in class net.sf.basedb.clients.jobagent.slotmanager.InternalSlotManager

log - Static variable in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager

log - Static variable in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager

log - Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl

log - Static variable in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor

log - Static variable in class net.sf.basedb.clients.web.extensions.service.Services

log - Static variable in class net.sf.basedb.clients.web.extensions.service.ServicesEventHandler

log - Static variable in class net.sf.basedb.clients.web.extensions.service.StartServiceRenderer

log - Static variable in class net.sf.basedb.clients.web.extensions.service.StopServiceRenderer

log - Variable in class net.sf.basedb.clients.web.extensions.XJspCompiler

log - Static variable in class net.sf.basedb.clients.web.fileupload.FileUpload

Debug file upload.

log - Static variable in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyReportServlet

log - Static variable in class net.sf.basedb.clients.web.taglib.DeprecationLogger

log - Static variable in class net.sf.basedb.core.AnnotationBatcher

log - Static variable in class net.sf.basedb.core.Application

Log core events.

log - Static variable in class net.sf.basedb.core.DbControl

Log core events.

log - Static variable in class net.sf.basedb.core.DynamicResultIterator

Logger.

log - Static variable in class net.sf.basedb.core.ExtendedProperties

Log core events.

log - Static variable in class net.sf.basedb.core.hibernate.DbIndexWork

log - Static variable in class net.sf.basedb.core.hibernate.SchemaGenerator

log - Static variable in class net.sf.basedb.core.HibernateUtil

Log core events.

log - Static variable in class net.sf.basedb.core.Install

Log core events.

log - Static variable in class net.sf.basedb.core.InternalJobQueue

Log job queue events.

log - Static variable in class net.sf.basedb.core.JobAgent

Log events.

log - Static variable in class net.sf.basedb.core.Keyring

Log core events.

log - Static variable in class net.sf.basedb.core.PredefinedQuery

Log core events.

log - Static variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager

log - Static variable in class net.sf.basedb.core.query.Hql

Log core events.

log - Static variable in class net.sf.basedb.core.RawDataTypes

Log core events.

log - Static variable in class net.sf.basedb.core.ServiceSessionControl

log - Static variable in class net.sf.basedb.core.SessionControl

Log core events.

log - Static variable in class net.sf.basedb.core.Trashcan

Log trashcan events.

log - Static variable in class net.sf.basedb.core.Update

Log core events.

log - Variable in class net.sf.basedb.util.ColorGenerator

log - Variable in class net.sf.basedb.util.extensions.logging.ExtensionsLogger

log - Static variable in class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory

log - Static variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile

log - Static variable in class net.sf.basedb.util.extensions.manager.ExtensionsManager

log - Static variable in class net.sf.basedb.util.extensions.manager.filter.DeletedFilter

log - Static variable in class net.sf.basedb.util.extensions.manager.filter.InstalledFilter

log - Static variable in class net.sf.basedb.util.extensions.manager.filter.InvalidAndModifiedFilter

log - Static variable in class net.sf.basedb.util.extensions.manager.filter.ValidAndNewOrModifiedFilter

log - Static variable in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor

log - Static variable in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor

log - Static variable in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor

log - Static variable in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor

log - Static variable in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor

log - Static variable in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor

log - Static variable in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor

log - Static variable in class net.sf.basedb.util.extensions.Registry

log - Static variable in class net.sf.basedb.util.extensions.RethrowErrorHandlerFactory

log - Static variable in class net.sf.basedb.util.extensions.xml.ExtensionPointFilter

log - Static variable in class net.sf.basedb.util.extensions.xml.XmlLoader

log - Static variable in class net.sf.basedb.util.JarClassLoader

log - Static variable in class net.sf.basedb.util.overview.GenericOverview

log - Static variable in class net.sf.basedb.util.overview.loader.AbstractNodeLoader

log - Static variable in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader

log - Static variable in class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory

log - Static variable in class net.sf.basedb.util.overview.node.NodeFactory

log - Static variable in class net.sf.basedb.util.resources.ResourceBundleWrapper

log - Static variable in class net.sf.basedb.util.StaticCache

Log static cache events.

log - Static variable in class net.sf.basedb.util.timer.ThreadTimerTask

log - Static variable in class net.sf.basedb.util.XmlUtil2

Log core events.

log(double, Expression) - Static method in class net.sf.basedb.core.query.Expressions

Calculate the n-based logarithm of an expression: new expression = log(n, e).

log(String) - Method in class net.sf.basedb.core.plugin.AbstractPlugin

Log a message to the log file created by AbstractPlugin.createLogFile(String).

log(String, Throwable) - Method in class net.sf.basedb.core.plugin.AbstractPlugin

Log a message and stack trace to the log file created by AbstractPlugin.createLogFile(String).

log(String, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

Log a message about a data line to the log file created by AbstractPlugin.createLogFile(String).

log(String, FlatFileParser.Data, Throwable) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

Log an error message about a data line to the log file created by AbstractPlugin.createLogFile(String).

log(String, FlatFileParser.Line) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

Log a message about a header line to the log file created by AbstractPlugin.createLogFile(String).

log(String, FlatFileParser.Line, Throwable) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

Log an error message about a header line to the log file created by AbstractPlugin.createLogFile(String).

log(ChangeHistoryData) - Method in class net.sf.basedb.core.LogControl

Add a main entry the change history table.

log(ChangeHistoryDetailData) - Method in class net.sf.basedb.core.LogControl

Adds information about a modified entity to the change history table.

log(LogLevel, String) - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLogger

Log a message at the specified level.

log(LogLevel, String, Throwable) - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLogger

Log a message at the specified level with an optional stacktrace.

log(Logger, String, Throwable) - Method in enum class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory.Level

log10(Expression) - Static method in class net.sf.basedb.core.query.Expressions

Calculate the 10-based logarithm of an expression: new expression = log10(e).

LOG10 - Enum constant in enum class net.sf.basedb.core.IntensityTransform

Spot intensities are stored as base-10 logged values

LOG10_2 - Static variable in class net.sf.basedb.util.ma.Log10MACalculator

Log10MACalculator - Class in net.sf.basedb.util.ma

MA calculator for log2-transformed spot intensity values.

Log10MACalculator() - Constructor for class net.sf.basedb.util.ma.Log10MACalculator

log2(Number) - Method in class net.sf.basedb.util.jep.Log2Function

Calculate the 2-based logarithm of the argument.

log2(Expression) - Static method in class net.sf.basedb.core.query.Expressions

Calculate the 2-based logarithm of an expression: new expression = log2(e).

LOG2 - Enum constant in enum class net.sf.basedb.core.IntensityTransform

Spot intensities are stored as base-2 logged values

LOG2 - Static variable in class net.sf.basedb.util.jep.Log2Function

The natural logarithm of 2.

Log2Function - Class in net.sf.basedb.util.jep

A JEP function class that adds a log2(expression) function to a JEP expression parser.

Log2Function() - Constructor for class net.sf.basedb.util.jep.Log2Function

Create a new instance of this function.

Log2MACalculator - Class in net.sf.basedb.util.ma

MA calculator for log2-transformed spot intensity values.

Log2MACalculator() - Constructor for class net.sf.basedb.util.ma.Log2MACalculator

LogarithmConverter - Class in net.sf.basedb.util.jep.convert

Convert Logarithm function to a Query API Expression.

LogarithmConverter() - Constructor for class net.sf.basedb.util.jep.convert.LogarithmConverter

logarithmic - Variable in class net.sf.basedb.core.data.ColoringData

logChangeDetails(Collection<ChangeHistoryDetailData>, EntityDetails) - Method in class net.sf.basedb.core.log.db.DbLogManager

Log the given details to the database.

logChangeDetails(ChangeHistoryDetailData, EntityDetails) - Method in class net.sf.basedb.core.log.db.DbLogManager

Log the given details to the database.

logChanges(LogManager, EntityDetails) - Method in class net.sf.basedb.core.log.db.AnnotationLogger

logChanges(LogManager, EntityDetails) - Method in class net.sf.basedb.core.log.db.AnnotationSetLogger

logChanges(LogManager, EntityDetails) - Method in class net.sf.basedb.core.log.db.AnyToAnyLogger

logChanges(LogManager, EntityDetails) - Method in class net.sf.basedb.core.log.db.BioMaterialEventLogger

logChanges(LogManager, EntityDetails) - Method in class net.sf.basedb.core.log.db.DefaultEntityLogger

Creates a new ChangeHistoryDetailData and saves it to DbLogManager.logChangeDetails(ChangeHistoryDetailData, EntityDetails).

logChanges(LogManager, EntityDetails) - Method in class net.sf.basedb.core.log.db.FileSetMemberLogger

logChanges(LogManager, EntityDetails) - Method in class net.sf.basedb.core.log.db.ManualEntryLogger

logChanges(LogManager, EntityDetails) - Method in class net.sf.basedb.core.log.db.PlateEventLogger

logChanges(LogManager, EntityDetails) - Method in interface net.sf.basedb.core.log.EntityLogger

Called when changes has been detected to an entity.

logChanges(LogManager, EntityDetails) - Method in class net.sf.basedb.core.MigrateRbaToDba.MigratedLogger

logChangeType - Variable in enum class net.sf.basedb.core.AnnotationBatcher.Change

logControl - Variable in class net.sf.basedb.core.DbControl

Handles logging of changes to items.

logControl - Variable in class net.sf.basedb.core.log.db.DbLogManager

logControl - Variable in class net.sf.basedb.core.log.LoggingInterceptor

logControl - Variable in class net.sf.basedb.core.log.TransactionDetails

LogControl - Class in net.sf.basedb.core

Gives information about the current transaction and gives log implementations limited access to the database.

LogControl(DbControl) - Constructor for class net.sf.basedb.core.LogControl

logDc - Variable in class net.sf.basedb.core.plugin.AbstractPlugin

LogDetails(LogManager, EntityLogger, EntityDetails) - Constructor for class net.sf.basedb.core.log.LoggingInterceptor.LogDetails

logEntries - Variable in class net.sf.basedb.util.extensions.logging.ExtensionsLog

logEntry(ManualLogEntry) - Method in class net.sf.basedb.core.DbControl

Add a manual log entry to the history log.

LogEntry - Class in net.sf.basedb.util.extensions.logging

An entry in the log.

LogEntry(LogLevel, String, Throwable) - Constructor for class net.sf.basedb.util.extensions.logging.LogEntry

LogExpression - Class in net.sf.basedb.core.query

Take the n-based logarithm of an expression: log(n, e).

LogExpression(double, Expression) - Constructor for class net.sf.basedb.core.query.LogExpression

logfile - Variable in class net.sf.basedb.core.plugin.AbstractPlugin

LOGFILE_PARAMETER - Static variable in class net.sf.basedb.plugins.util.Parameters

The name of the parameter that is created by Parameters.logFileParameter(String, String, String)

logFileParameter(String, String, String) - Static method in class net.sf.basedb.plugins.util.Parameters

Parameter definition that asks for the path to a log file that a plug-in can use for logging detailed information about it's progress.

LoggableData - Interface in net.sf.basedb.core.data

Tagging interface that should be implemented by all data classes that we want to log in the change history tables.

loggableWithoutValues - Variable in class net.sf.basedb.core.log.EntityLogOptions

LoggableWithoutValues - Annotation Interface in net.sf.basedb.core.data

Getter methods that are annotated with this annotation should not have their old/new values logged in the change history log.

logger - Static variable in class net.sf.basedb.clients.web.util.SimpleSignalProgressReporter

Log signals processing.

logger - Variable in class net.sf.basedb.core.log.LoggingInterceptor.LogDetails

logger - Variable in class net.sf.basedb.core.plugin.AbstractPlugin

logger - Static variable in class net.sf.basedb.core.signal.AbstractSignalReceiver

Log signals processing.

logger - Static variable in class net.sf.basedb.core.signal.AbstractSignalTransporter

Log signals processing.

logger - Static variable in class net.sf.basedb.core.signal.DelegatingSignalHandler

Log signals processing.

logger - Static variable in class net.sf.basedb.core.signal.EnhancedThreadSignalHandler

Log signals processing.

logger - Static variable in class net.sf.basedb.core.signal.ExtensionSignalTransporter

logger - Static variable in class net.sf.basedb.core.signal.ForwardingSignalHandler

Log signals processing.

logger - Static variable in class net.sf.basedb.core.signal.LocalSignalReceiver

Log signals processing.

logger - Static variable in class net.sf.basedb.core.signal.LocalSignalTransporter

Log signals processing.

logger - Static variable in class net.sf.basedb.core.signal.ProgressReporterSignalHandler

Log signals processing.

logger - Static variable in class net.sf.basedb.core.signal.SocketSignalReceiver

Log signals processing.

logger - Static variable in class net.sf.basedb.core.signal.SocketSignalTransporter

Log signals processing.

logger - Static variable in class net.sf.basedb.core.signal.ThreadSignalHandler

Log signals processing.

logger - Variable in class net.sf.basedb.util.jobagent.JobAgentServerConnection.ListenerThread

logger - Variable in class net.sf.basedb.util.jobagent.JobAgentServerConnection

logger - Variable in class net.sf.basedb.util.jobagent.JobAgentServerConnection.RequestHandlerThread

LoggingErrorHandlerFactory - Class in net.sf.basedb.util.extensions

Exception handler factory implementation that logs error messages using the default logging mechanism.

LoggingErrorHandlerFactory() - Constructor for class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory

Create a new error-level loggin error handler factory.

LoggingErrorHandlerFactory(String) - Constructor for class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory

Create a new custom-level logging error handler factory.

LoggingErrorHandlerFactory.Level - Enum Class in net.sf.basedb.util.extensions

Log level implementations for slf4j.

loggingInterceptor - Variable in class net.sf.basedb.core.AnnotationBatcher

LoggingInterceptor - Class in net.sf.basedb.core.log

Interceptor that attaches to Hibernate sessions to provide logging of items that are updated/created/deleted.

LoggingInterceptor(LogControl, ExtensionsInvoker<LogManagerFactory>) - Constructor for class net.sf.basedb.core.log.LoggingInterceptor

Creates a new interceptor.

LoggingInterceptor.LogDetails - Class in net.sf.basedb.core.log

LoggingInterceptor.LogManagerAndFactory - Class in net.sf.basedb.core.log

logHandlers - Variable in class net.sf.basedb.core.log.LoggingInterceptor

login - Variable in class net.sf.basedb.clients.jobagent.Agent

login - Variable in class net.sf.basedb.core.authentication.AuthenticatedUser

login - Variable in class net.sf.basedb.core.authentication.LoginRequest

login - Variable in class net.sf.basedb.core.data.UserData

login(LoginRequest) - Method in class net.sf.basedb.core.PluginSessionControl

login(LoginRequest) - Method in class net.sf.basedb.core.SessionControl

Log in to BASE.

login(Keyring) - Method in class net.sf.basedb.core.PluginSessionControl

login(Keyring) - Method in class net.sf.basedb.core.SessionControl

loginComment - Variable in class net.sf.basedb.core.data.SessionData

LoginException - Exception in net.sf.basedb.core.authentication

This exception can be thrown when an error occurs during the authentication, but it is not known if the username or password is causing the problem.

LoginException - Exception in net.sf.basedb.core

Exceptions of this type are thrown when the BASE server uses an external authentication plug-in and it is not clear if the login or password is causing the failure.

LoginException(String) - Constructor for exception net.sf.basedb.core.authentication.LoginException

Create a new LoginException object

LoginException(String) - Constructor for exception net.sf.basedb.core.LoginException

Create a new LoginException object with the specified message

LoginException(String, Throwable) - Constructor for exception net.sf.basedb.core.authentication.LoginException

Create a new LoginException object

LoginException(String, Throwable) - Constructor for exception net.sf.basedb.core.LoginException

Create a new LoginException object with the specified message

loginField - Variable in class net.sf.basedb.clients.web.extensions.login.LoginFormBean

logInfo - Variable in class net.sf.basedb.core.log.ManualLogEntry

LoginFormAction - Interface in net.sf.basedb.clients.web.extensions.login

An action for customizing the login form.

LoginFormBean - Class in net.sf.basedb.clients.web.extensions.login

A simple implementation of the LoginFormAction interface.

LoginFormBean() - Constructor for class net.sf.basedb.clients.web.extensions.login.LoginFormBean

loginInfo - Variable in class net.sf.basedb.core.SessionControl

Login information for the logged in user.

LoginInfo() - Constructor for class net.sf.basedb.core.SessionControl.LoginInfo

LoginInfo(SessionControl.LoginInfo) - Constructor for class net.sf.basedb.core.SessionControl.LoginInfo

loginIsUsed(DbControl, String) - Static method in class net.sf.basedb.core.User

Check if a login name already exists in the database

loginRequest - Variable in class net.sf.basedb.core.AuthenticationContext

loginRequest - Variable in class net.sf.basedb.core.SessionControl.UnverifiedDeviceInfo

LoginRequest - Class in net.sf.basedb.core.authentication

Hold information about a login request such as login, password, etc.

LoginRequest() - Constructor for class net.sf.basedb.core.authentication.LoginRequest

LoginRequest(int, String) - Constructor for class net.sf.basedb.core.authentication.LoginRequest

Create a login request with user id + password

LoginRequest(int, String, String) - Constructor for class net.sf.basedb.core.authentication.LoginRequest

Create a login request with user id + password + deviceToken

LoginRequest(String, String) - Constructor for class net.sf.basedb.core.authentication.LoginRequest

Create a login request with login + password

LoginRequest(String, String, String) - Constructor for class net.sf.basedb.core.authentication.LoginRequest

Create a login request with login + password + deviceToken

logInterceptor - Variable in class net.sf.basedb.core.DbControl

logInterceptor - Variable in class net.sf.basedb.core.MigrateRbaToDba

loginTime - Variable in class net.sf.basedb.core.data.SessionData

logInvoker - Variable in class net.sf.basedb.core.log.LoggingInterceptor

LogLevel - Enum Class in net.sf.basedb.util.extensions.logging

The level of the log message.

LogLevel(String) - Constructor for enum class net.sf.basedb.util.extensions.logging.LogLevel

LogManager - Interface in net.sf.basedb.core.log

Manages the logging of changes made in a single transaction.

LogManagerAndFactory(LogManagerFactory, LogManager) - Constructor for class net.sf.basedb.core.log.LoggingInterceptor.LogManagerAndFactory

LogManagerFactory - Interface in net.sf.basedb.core.log

A log manager factory handles the creation of log managers and entity loggers.

logOptions - Variable in class net.sf.basedb.core.log.EntityDetails

logout() - Method in class net.sf.basedb.core.PluginSessionControl

Do nothing, a plugin is not allowed to log out.

logout() - Method in class net.sf.basedb.core.SessionControl

Log out of BASE.

logoutTime - Variable in class net.sf.basedb.core.data.SessionData

logParam - Static variable in class net.sf.basedb.core.AbstractEntityQuery

Log all parameter bindings to prepared statement.

logParam - Static variable in class net.sf.basedb.core.AbstractHqlQuery

Log all parameter bindings to prepared statement.

logParam - Static variable in class net.sf.basedb.core.AbstractSqlQuery

Log all parameter bindings to prepared statement.

logParam - Static variable in class net.sf.basedb.core.BasicBatcher

Log all parameter bindings to prepared statement.

logs - Static variable in class net.sf.basedb.util.extensions.logging.ExtensionsLog

logServer - Static variable in class net.sf.basedb.clients.jobagent.Agent

Log job agent server events.

logSql - Static variable in class net.sf.basedb.core.AbstractBatcher

Log all SQL statements.

logSql - Static variable in class net.sf.basedb.core.AbstractQuery

Log all SQL statements.

logSql - Static variable in class net.sf.basedb.core.AbstractSqlQuery

Log all SQL statements.

logSql - Static variable in class net.sf.basedb.core.AnnotationRestriction

Log all SQL statements.

logSql - Static variable in class net.sf.basedb.core.BatchUtil

Log all SQL statements.

logSql - Static variable in class net.sf.basedb.core.HibernateUtil

Log all batcher SQL statements.

logSql - Static variable in class net.sf.basedb.core.RawDataBatcher

Log all SQL statements.

logSql - Static variable in class net.sf.basedb.core.VirtualDb

Log all SQL statements.

logSQLExceptionChain(Logger, SQLException) - Static method in class net.sf.basedb.core.LogUtil

Log the chained exceptions of an SQLException.

logTo(Logger, String, Throwable) - Method in enum class net.sf.basedb.util.extensions.logging.LogLevel

LogUtil - Class in net.sf.basedb.core

Utility class for LOG4J logging.

LogUtil() - Constructor for class net.sf.basedb.core.LogUtil

LONG - Enum constant in enum class net.sf.basedb.core.Job.ExecutionTime

The job takes more than 1 hour to execute.

LONG - Enum constant in enum class net.sf.basedb.core.Type

Long integer type.

LONG - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper

LONG_LINK_FLAG - Static variable in class net.sf.basedb.util.zip.TarUtil

The TAR header flag that must be set for @LongLink entries.

LONG_LINK_NAME - Static variable in class net.sf.basedb.util.zip.TarUtil

TAR has a limit of 100 characters in file names.

longitude - Variable in class net.sf.basedb.util.GeoLocation

LongParameterType - Class in net.sf.basedb.core

This class represent a parameter type that is a long.

LongParameterType() - Constructor for class net.sf.basedb.core.LongParameterType

Create a new long parameter type, without any limits and allowing null values.

LongParameterType(Long, Long, Long, boolean) - Constructor for class net.sf.basedb.core.LongParameterType

Create a new long parameter type.

LongParameterType(Long, Long, Long, boolean, int, int, int, List<Long>) - Constructor for class net.sf.basedb.core.LongParameterType

LongParameterValueData - Class in net.sf.basedb.core.data

Long parameter value.

LongParameterValueData() - Constructor for class net.sf.basedb.core.data.LongParameterValueData

LongParameterValueData(Long...) - Constructor for class net.sf.basedb.core.data.LongParameterValueData

longValues - Variable in class net.sf.basedb.util.formatter.IntegerFormatter

LongWriter - Class in net.sf.basedb.core.migrate

Database-independent writer implementation that writes long values from a result set.

LongWriter(ResultSet, int, Writer, char[]) - Constructor for class net.sf.basedb.core.migrate.LongWriter

LookupFormatter<T> - Class in net.sf.basedb.util.formatter

A formatter implementation that uses a map to lookup values from a set of keys.

LookupFormatter() - Constructor for class net.sf.basedb.util.formatter.LookupFormatter

Create a new lookup formatter

LookupFormatter(Map<? extends T, ? extends String>) - Constructor for class net.sf.basedb.util.formatter.LookupFormatter

Create a new lookup formatter and initialise it with the key-value pairs in the given map.

LookupFormatter(Enumeration<? extends T, ? extends String>) - Constructor for class net.sf.basedb.util.formatter.LookupFormatter

Create a new lookup formatter and initialise it with the key-value pairs in the given enumeration.

lookupUnitInDb(UnitCache.CacheKey, boolean) - Method in class net.sf.basedb.util.units.UnitCache

Lookup a unit in the database and optionally add it to the cache.

low - Variable in class net.sf.basedb.core.query.BetweenRestriction

lowerLimit - Variable in class net.sf.basedb.core.DoubleParameterType

The lower limit of the parameter.

lowerLimit - Variable in class net.sf.basedb.core.FloatParameterType

The lower limit of the parameter.

lowerLimit - Variable in class net.sf.basedb.core.IntegerParameterType

The lower limit of the parameter.

lowerLimit - Variable in class net.sf.basedb.core.LongParameterType

The lower limit of the parameter.

lowess(List<LowessNormalization.SpotData>, double, int, double) - Static method in class net.sf.basedb.plugins.LowessNormalization

LowessNormalization - Class in net.sf.basedb.plugins

LowessNormalization() - Constructor for class net.sf.basedb.plugins.LowessNormalization

LowessNormalization.CallableWorker - Class in net.sf.basedb.plugins

LowessNormalization.SpotData - Class in net.sf.basedb.plugins

lowessSection - Static variable in class net.sf.basedb.plugins.LowessNormalization

Section for lowess options

lowExcludeParameter - Static variable in class net.sf.basedb.plugins.MedianRatioNormalization

lowValue - Variable in class net.sf.basedb.core.AnnotationBetweenRestriction

lt(Expression, Expression) - Static method in class net.sf.basedb.core.query.Restrictions

Compare if one expression is less than another: new restriction = e1 < e2.

LT - Enum constant in enum class net.sf.basedb.core.Operator

LT - Static variable in class net.sf.basedb.clients.web.util.HTML

lteq(Expression, Expression) - Static method in class net.sf.basedb.core.query.Restrictions

Compare if one expression is less than or equal to another: new restriction = e1 <= e2.

LTEQ - Enum constant in enum class net.sf.basedb.core.Operator

LteqRestriction - Class in net.sf.basedb.core.query

Compare if one expression is less than or equal to another: e1 <= e2.

LteqRestriction(Expression, Expression) - Constructor for class net.sf.basedb.core.query.LteqRestriction

LtRestriction - Class in net.sf.basedb.core.query

Compare if one expression is less than another: e1 < e2.

LtRestriction(Expression, Expression) - Constructor for class net.sf.basedb.core.query.LtRestriction

M

M - Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData

M - Variable in class net.sf.basedb.plugins.MedianRatioNormalization.SpotData

MA(double, double) - Method in class net.sf.basedb.util.ma.Log10MACalculator

M = (ch1 - ch2) / log10(2) A = (ch1 + ch2) / 2

MA(double, double) - Method in class net.sf.basedb.util.ma.Log2MACalculator

M = ch1 - ch2 A = (ch1 + ch2) / (2 * log2(10))

MA(double, double) - Method in class net.sf.basedb.util.ma.MACalculator

Calculate the M and A values from the ch1 and ch2 intensity values.

mac - Variable in class net.sf.basedb.plugins.LowessNormalization.CallableWorker

MACalculator - Class in net.sf.basedb.util.ma

Calculates M and A values for 2-channel data.

MACalculator() - Constructor for class net.sf.basedb.util.ma.MACalculator

MAGNETIC_FIELD - Static variable in class net.sf.basedb.core.Quantity

The id for the Quantity object representing magnetic field.

MAGNETIC_FLUX - Static variable in class net.sf.basedb.core.Quantity

The id for the Quantity object representing magnetic flux.

main(String[]) - Static method in class net.sf.basedb.clients.jobagent.AgentController

main(String[]) - Static method in class net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor

mainContext - Variable in class net.sf.basedb.util.extensions.ExtensionContext

MainContext(Item) - Constructor for class net.sf.basedb.core.SessionControl.MainContext

mainDir - Variable in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor

mainDir - Variable in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor

mainJarFile - Variable in class net.sf.basedb.util.JarClassLoader

The main JAR file to load classes from.

maintenance - Static variable in class net.sf.basedb.core.Version

mainType - Variable in class net.sf.basedb.core.data.PluginDefinitionData

MainType(int, String) - Constructor for enum class net.sf.basedb.core.plugin.Plugin.MainType

major - Static variable in class net.sf.basedb.core.Version

makeSafe(String) - Method in class net.sf.basedb.core.dbengine.TableInfo

Sometime the database put quotes around names.

makeSafeCreateTable(String, String, String, String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine

Return the SQL unmodified.

makeSafeCreateTable(String, String, String, String) - Method in interface net.sf.basedb.core.dbengine.DbEngine

Create a "safe" CREATE TABLE query string that will not fail if the table already exists.

makeSafeCreateTable(String, String, String, String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine

Replace "create table" with "create table if not exists"...

makeSafeFilename(String, String) - Static method in class net.sf.basedb.core.Path

Convert a string to a name that is safe to use as a filename.

makeSafeHeaderValue(String) - Method in class net.sf.basedb.plugins.GalExporter

Removes "unsafe" characters in the value.

makeUnique(String) - Method in class net.sf.basedb.util.bfs.AbstractFilenameGenerator

Make sure that a file name is unique.

makeValidKey(String, String) - Static method in class net.sf.basedb.util.StaticCache

Convert a possible invalid cache key to a valid one by replacing invalid characters with the replacement string.

manager - Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl

manager - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper

manager - Variable in class net.sf.basedb.core.log.LoggingInterceptor.LogDetails

manager - Variable in class net.sf.basedb.core.log.LoggingInterceptor.LogManagerAndFactory

manager - Variable in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil

manager - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile

manager - Variable in class net.sf.basedb.util.extensions.manager.Settings

mandatory - Variable in class net.sf.basedb.core.data.ReporterClonePropertyData

MANDATORY - Static variable in class net.sf.basedb.core.ClonableProperty

manifest - Variable in class net.sf.basedb.util.JarClassLoader.JarInfo

manipulateDocument(Document, HibernateUtil.FilterConfigurator) - Static method in class net.sf.basedb.core.HibernateUtil

Some XML files require manipulation by us before they are registered.

ManualDerivedBioAssayCreator - Class in net.sf.basedb.plugins

Plug-in that allows a user to manually register an external analysis procedure for derived bioassays and to upload files that was generated by it.

ManualDerivedBioAssayCreator() - Constructor for class net.sf.basedb.plugins.ManualDerivedBioAssayCreator

ManualEntryLogger - Class in net.sf.basedb.core.log.db

Logger for manual entries.

ManualEntryLogger(DbLogManagerFactory) - Constructor for class net.sf.basedb.core.log.db.ManualEntryLogger

Creates a new plate event logger.

ManualLogEntry - Class in net.sf.basedb.core.log

Represents a manual entry into the change history log.

ManualLogEntry(BasicItem, ChangeType, String) - Constructor for class net.sf.basedb.core.log.ManualLogEntry

Create a new log entry.

ManualLogEntry(BasicItem, ChangeType, String, String, String) - Constructor for class net.sf.basedb.core.log.ManualLogEntry

Create a new log entry with optional old and new values.

ManualTransformCreator - Class in net.sf.basedb.plugins

Plug-in that allows a user to manually register an external analysis procedure and to upload files that was generated by it.

ManualTransformCreator() - Constructor for class net.sf.basedb.plugins.ManualTransformCreator

map - Variable in class net.sf.basedb.clients.web.extensions.skin.ImageRemapper

map - Variable in class net.sf.basedb.util.formatter.LookupFormatter

map(String, String) - Method in class net.sf.basedb.clients.web.extensions.skin.ImageRemapper

Remap a source image to a destination image.

MAParser - Class in net.sf.basedb.util.importer.spotdata

Spot intensity parser implementation for 2-channel data that looks for M/A values in the spot data and converts them to ch1/ch2 intensity values.

MAParser() - Constructor for class net.sf.basedb.util.importer.spotdata.MAParser

Creates a new MA-parser.

mapKey - Variable in class net.sf.basedb.clients.web.plugins.MapValueLoader

MAPlotFactory - Class in net.sf.basedb.clients.web.extensions.plot

Factory for generating MA and correction factor plots for 2-channel data.

MAPlotFactory() - Constructor for class net.sf.basedb.clients.web.extensions.plot.MAPlotFactory

mapParentChildColumns(short, short) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo

Maps a parent data cube column to a child cube column.

mapper - Variable in class net.sf.basedb.plugins.batchimport.UsedQuantityMapper

Mapper - Interface in net.sf.basedb.util.parser

Represents a mapping expression that gets a single value from a line of data.

mappers - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

mappers - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter.BatchAndMapHolder

mappers - Variable in class net.sf.basedb.util.parser.CompoundMapper

mapping - Variable in class net.sf.basedb.core.MigrateRbaToDba

mapping - Variable in class net.sf.basedb.plugins.PlateMappingExporter

MAPPING - Enum constant in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section

mappingBatcher - Variable in class net.sf.basedb.core.DataCube

MappingBatcher - Class in net.sf.basedb.core

Batcher class for inserting parent mapping information in the dynamic database.

MappingBatcher(DbControl, DataCube) - Constructor for class net.sf.basedb.core.MappingBatcher

Create a new position batcher for a data cube.

MappingCoordinate - Class in net.sf.basedb.core.data

This class defines a mapping coordinate, which is a triplet of plate number, row and column.

MappingCoordinate() - Constructor for class net.sf.basedb.core.data.MappingCoordinate

Create new object.

MappingCoordinate(int, int, int) - Constructor for class net.sf.basedb.core.data.MappingCoordinate

Create new MappingCoordinate with the specified plate, row and column.

mappings - Variable in class net.sf.basedb.core.data.VirtualDbData

mappingSection - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter

Section definition for grouping all column mapping expressions

MapPropertyPath(Type) - Constructor for class net.sf.basedb.core.Metadata.MapPropertyPath

mapToSubtype(MigrateRbaToDba.Itemlist) - Method in class net.sf.basedb.core.MigrateRbaToDba.SubtypeMapping

Map a subtype to the given item list.

mapToSubtype(MigrateRbaToDba.Rba) - Method in class net.sf.basedb.core.MigrateRbaToDba.SubtypeMapping

Map a subtype to the given raw bioassay.

MapValueLoader - Class in net.sf.basedb.clients.web.plugins

Data loader implementation that load values from a map collection.

MapValueLoader(Metadata.PropertyPath<BasicItem, Map<?, ?>>, Object) - Constructor for class net.sf.basedb.clients.web.plugins.MapValueLoader

Load values from a map.

mapZeroToNull - Variable in class net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser

mark(int) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream

Not supported.

mark(int) - Method in class net.sf.basedb.util.InputStreamSplitter

mark(int) - Method in class net.sf.basedb.util.InputStreamTracker

markAsProcessed() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile

Mark the file as fully processed by the extensions manager.

MarkAsProcessedProcessor - Class in net.sf.basedb.util.extensions.manager.processor

File processor implementation that marks all extension files as processed.

MarkAsProcessedProcessor() - Constructor for class net.sf.basedb.util.extensions.manager.processor.MarkAsProcessedProcessor

markSupported() - Method in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream

Not supported.

markSupported() - Method in class net.sf.basedb.util.gtf.GtfInputStream

markSupported() - Method in class net.sf.basedb.util.InputStreamSplitter

markSupported() - Method in class net.sf.basedb.util.InputStreamTracker

MARKUP - Static variable in class net.sf.basedb.clients.web.util.HTML

Pattern that matches everything inside a HTML tag.

masked - Variable in class net.sf.basedb.core.data.ParameterValueData

masked - Variable in class net.sf.basedb.core.ParameterInfo

MASS - Static variable in class net.sf.basedb.core.Quantity

The id for the Quantity object representing mass.

master - Variable in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlotRequestHandler

master - Variable in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlotTimeoutChecker

master - Variable in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager.RemoteSlotPinger

master - Variable in class net.sf.basedb.util.ChainedProgressReporter

master - Variable in class net.sf.basedb.util.gtf.GtfInputStream

master - Variable in class net.sf.basedb.util.jep.ReporterFunction

master - Variable in class net.sf.basedb.util.StreamCacher

masterParser - Variable in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser

MasterReporterJoiner(JoinType) - Constructor for class net.sf.basedb.core.DynamicReporterQuery.MasterReporterJoiner

MasterSlotManager - Class in net.sf.basedb.clients.jobagent.slotmanager

An extension to the internal slot manager which also accepts slot assignment from remote job agents.

MasterSlotManager() - Constructor for class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager

MasterSlotManager.RemoteSlot - Class in net.sf.basedb.clients.jobagent.slotmanager

A remote slot is a slot with some information about when it was created and last updated.

MasterSlotManager.RemoteSlotRequestHandler - Class in net.sf.basedb.clients.jobagent.slotmanager

Request handler implementation that accepts requests for slots from remote hosts.

MasterSlotManager.RemoteSlotTimeoutChecker - Class in net.sf.basedb.clients.jobagent.slotmanager

Task that is scheduled at regular intervals to check for timed out slots.

matcher - Variable in class net.sf.basedb.util.fuzzy.StringMatcher

matches(MigrateRbaToDba.Itemlist) - Method in class net.sf.basedb.core.MigrateRbaToDba.LineMapping

matches(MigrateRbaToDba.Rba) - Method in class net.sf.basedb.core.MigrateRbaToDba.LineMapping

matching - Variable in class net.sf.basedb.core.SyncFilter

matchingMd5 - Variable in class net.sf.basedb.core.SyncFilter

matchingReporters - Variable in class net.sf.basedb.clients.web.ExperimentExplorer

Number of reporter that match the reporter search.

matchingSource - Variable in class net.sf.basedb.core.data.ItemListSyncFilterData

matchingTransformed - Variable in class net.sf.basedb.core.data.ItemListSyncFilterData

MatrixBaseFileExporter - Class in net.sf.basedb.util.export.spotdata

Exporter implementation that exports bioassay set data as a matrix BASEfile.

MatrixBaseFileExporter() - Constructor for class net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter

Create a new matrix BASEfile exporter.

MatrixBfsExporter - Class in net.sf.basedb.util.export.spotdata

BFS exporter implementation that exports spot data in matrix format.

MatrixBfsExporter() - Constructor for class net.sf.basedb.util.export.spotdata.MatrixBfsExporter

Create a new matrix BFS exporter.

MatrixModel - Class in net.sf.basedb.util.bfs

A model container for BFS data files.

MatrixModel() - Constructor for class net.sf.basedb.util.bfs.MatrixModel

Create a new annotation model.

MatrixSpotIntensityEventHandler - Class in net.sf.basedb.util.importer.spotdata

Event handler that extracts spot intensity information from matrix BFS data files and inserts the values to a spot batcher.

MatrixSpotIntensityEventHandler(SpotBatcher, PositionEventHandler, BioAssay[], int[]) - Constructor for class net.sf.basedb.util.importer.spotdata.MatrixSpotIntensityEventHandler

Create a new spot instensity event handler.

max - Variable in class net.sf.basedb.util.InputStreamTracker.CurvedScaleFactor

max - Variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin

max(Expression) - Static method in class net.sf.basedb.core.query.Aggregations

Calculates the maximum value of an expression: new expression = MAX(e)

MAX - Enum constant in enum class net.sf.basedb.core.Formula.AverageMethod

MAX - Enum constant in enum class net.sf.basedb.util.plot.HistogramPlot.YAggregate

Plot the maximum of all y-values for spots falling into each bin.

MAX_ABSTRACT_LENGTH - Static variable in class net.sf.basedb.core.data.ExperimentData

MAX_ABSTRACT_LENGTH - Static variable in class net.sf.basedb.core.Experiment

The maximum length of the abstract property that can be stored in the database.

MAX_ADDRESS_LENGTH - Static variable in class net.sf.basedb.core.data.UserData

The maximum length of the address that can be stored in the database.

MAX_ADDRESS_LENGTH - Static variable in class net.sf.basedb.core.User

The maximum length of the address that can be stored in the database.

MAX_AFFILIATIONS_LENGTH - Static variable in class net.sf.basedb.core.data.ExperimentData

MAX_AFFILIATIONS_LENGTH - Static variable in class net.sf.basedb.core.Experiment

The maximum length of the affiliations property that can be stored in the database.

MAX_AUTHENTICATION_METHOD - Static variable in class net.sf.basedb.core.data.SessionData

The maximum length of the authentication method that can be stored in the database.

MAX_AUTHORS_LENGTH - Static variable in class net.sf.basedb.core.data.ExperimentData

MAX_AUTHORS_LENGTH - Static variable in class net.sf.basedb.core.Experiment

The maximum length of the authors property that can be stored in the database.

MAX_BARCODE_LENGTH - Static variable in class net.sf.basedb.core.ArraySlide

The maximum length of the barcode that can be stored in the database.

MAX_BARCODE_LENGTH - Static variable in class net.sf.basedb.core.BioPlate

The maximum length of the barcode that can be stored in the database.

MAX_BARCODE_LENGTH - Static variable in class net.sf.basedb.core.data.ArraySlideData

MAX_BARCODE_LENGTH - Static variable in class net.sf.basedb.core.data.BioPlateData

The maximum length of the barcode that can be stored in the database.

MAX_BARCODE_LENGTH - Static variable in class net.sf.basedb.core.data.PlateData

The maximum length of the barcode that can be stored in the database.

MAX_BARCODE_LENGTH - Static variable in class net.sf.basedb.core.Plate

The maximum length of the barcode that can be stored in the database.

MAX_CERTIFICATE_LENGTH - Static variable in class net.sf.basedb.core.data.FileServerData

MAX_CERTIFICATE_LENGTH - Static variable in class net.sf.basedb.core.FileServer

The maximum length of the server certificate that can be stored in the database.

MAX_CHANGE_INFO_LENGTH - Static variable in class net.sf.basedb.core.data.ChangeHistoryDetailData

MAX_CHARSET_LENGTH - Static variable in class net.sf.basedb.core.data.FileData

MAX_CHARSET_LENGTH - Static variable in class net.sf.basedb.core.File

The maximum length of the character set that can be stored in the database.

MAX_CLASSNAME_LENGTH - Static variable in class net.sf.basedb.core.data.PluginDefinitionData

The maximum length of the class name that can be stored in the database.

MAX_CLASSNAME_LENGTH - Static variable in class net.sf.basedb.core.PluginDefinition

The maximum length of the class name that can be stored in the database.

MAX_COLUMN_LENGTH - Static variable in class net.sf.basedb.core.data.ReporterClonePropertyData

The maximum length of the column that can be stored in the database.

MAX_COMMAND_LENGTH - Static variable in class net.sf.basedb.core.data.JobData

The maximum allowed length of the execute command.

MAX_COMMENT_LENGTH - Static variable in class net.sf.basedb.core.BioMaterialEvent

The maximum length of the comment about this event.

MAX_COMMENT_LENGTH - Static variable in class net.sf.basedb.core.data.BioMaterialEventData

The maximum length of the comment about this event.

MAX_COMMENT_LENGTH - Static variable in class net.sf.basedb.core.data.PlateEventData

The maximum length of the comment about this event.

MAX_COMMENT_LENGTH - Static variable in class net.sf.basedb.core.PlateEvent

The maximum length of the comment about this event.

MAX_CONNECTION_MANAGER_FACTORY_LENGTH - Static variable in class net.sf.basedb.core.data.FileServerData

MAX_CONNECTION_MANAGER_FACTORY_LENGTH - Static variable in class net.sf.basedb.core.FileServer

The maximum length of the connection manager factory id that can be stored in the database.

MAX_CONTACT_LENGTH - Static variable in class net.sf.basedb.core.data.PluginDefinitionData

The maximum length of the contact information that can be stored in the database.

MAX_CONTACT_LENGTH - Static variable in class net.sf.basedb.core.PluginDefinition

The maximum length of the contact information that can be stored in the database.

MAX_COPYRIGHT_LENGTH - Static variable in class net.sf.basedb.core.data.PluginDefinitionData

The maximum length of the copyright notice that can be stored in the database.

MAX_COPYRIGHT_LENGTH - Static variable in class net.sf.basedb.core.PluginDefinition

The maximum length of the copyright notice that can be stored in the database.

MAX_DEFAULT_VALUE_LENGTH - Static variable in class net.sf.basedb.core.AnnotationType

The maximum length of the default value.

MAX_DEFAULT_VALUE_LENGTH - Static variable in class net.sf.basedb.core.data.AnnotationTypeData

MAX_DESCRIPTION_LENGTH - Static variable in interface net.sf.basedb.core.data.NameableData

The maximum length of the description of the item that can be stored in the database.

MAX_DESCRIPTION_LENGTH - Static variable in class net.sf.basedb.core.data.ParameterValueData

The maximum length of the description of the parameter that can be stored in the database.

MAX_DESCRIPTION_LENGTH - Static variable in class net.sf.basedb.core.data.PluginDefinitionData

The maximum length of the url that can be stored in the database.

MAX_DESCRIPTION_LENGTH - Static variable in interface net.sf.basedb.core.Nameable

The maximum length of the description.

MAX_EMAIL_LENGTH - Static variable in class net.sf.basedb.core.data.PluginDefinitionData

The maximum length of the email address that can be stored in the database.

MAX_EMAIL_LENGTH - Static variable in class net.sf.basedb.core.data.UserData

The maximum length of the email address that can be stored in the database.

MAX_EMAIL_LENGTH - Static variable in class net.sf.basedb.core.PluginDefinition

The maximum length of the email address that can be stored in the database.

MAX_EMAIL_LENGTH - Static variable in class net.sf.basedb.core.User

The maximum length of the email address that can be stored in the database.

MAX_EXPERIMENT_DESIGN_LENGTH - Static variable in class net.sf.basedb.core.data.ExperimentData

MAX_EXPERIMENT_DESIGN_LENGTH - Static variable in class net.sf.basedb.core.Experiment

The maximum length of the experimentDesign property that can be stored in the database.

MAX_EXPERIMENT_TYPE_LENGTH - Static variable in class net.sf.basedb.core.data.ExperimentData

MAX_EXPERIMENT_TYPE_LENGTH - Static variable in class net.sf.basedb.core.Experiment

The maximum length of the experimentType property that can be stored in the database.

MAX_EXTENSION_LENGTH - Static variable in class net.sf.basedb.core.data.DataFileTypeData

The maximum length of the file extension that can be stored in the database.

MAX_EXTENSION_LENGTH - Static variable in class net.sf.basedb.core.data.MimeTypeData

MAX_EXTENSION_LENGTH - Static variable in class net.sf.basedb.core.DataFileType

The maximum length of the file extension that can be stored in the database.

MAX_EXTENSION_LENGTH - Static variable in class net.sf.basedb.core.MimeType

The maximum length of the extension variable that can be stored in the database.

MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.AnnotationType

The maximum length of the external id that can be stored in the database.

MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.BioMaterial

The maximum length of the external id that can be stored in the database.

MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.Client

The maximum length of the external id variable that can be stored in the database.

MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.data.AnnotationTypeData

The maximum length of the external id that can be stored in the database.

MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.data.BioMaterialData

The maximum length of the external id that can be stored in the database.

MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.data.BioPlateData

The maximum length of the external id that can be stored in the database.

MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.data.ClientData

The maximum length of the external ID that can be stored in the database.

MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.data.DataFileTypeData

The maximum length of the external ID that can be stored in the database.

MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.data.ExtraValueTypeData

The maximum length of the external id that can be stored in the database.

MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.data.FeatureData

The maximum length of the external ID that can be stored in the database.

MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.data.HelpData

The maximum length of the external ID that can be stored in the database.

MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.data.ItemListData

The maximum length of the external ID that can be stored in the database.

MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.data.JobAgentData

The maximum length of the external ID that can be stored in the database.

MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.data.JobData

The maximum allowed length of the external ID.

MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.data.PlatformData

The maximum length of the external ID that can be stored in the database.

MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.data.PlatformVariantData

The maximum length of the external ID that can be stored in the database.

MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.data.ProtocolData

The maximum length of the external id that can be stored in the database.

MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.data.ReporterData

The maximum length of the external ID that can be stored in the database.

MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.data.ReporterListData

The maximum length of the external ID that can be stored in the database.

MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.data.UserData

The maximum length of the external ID that can be stored in the database.

MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.DataFileType

The maximum length of the external ID that can be stored in the database.

MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.ExtraValueType

The maximum length of the external id variable that can be stored in the database.

MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.Help

The maximum length of the external id variable that can be stored in the database.

MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.ItemList

The maximum length of the external id variable that can be stored in the database.

MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.Job

The maximum allowed length of the external ID.

MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.JobAgent

The maximum length of the external ID that can be stored in the database.

MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.Platform

The maximum length of the external ID that can be stored in the database.

MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.PlatformVariant

The maximum length of the external ID that can be stored in the database.

MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.Protocol

The maximum length of the external id that can be stored in the database.

MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.ReporterList

The maximum length of the external id variable that can be stored in the database.

MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.User

The maximum length of the external ID that can be stored in the database.

MAX_FAX_LENGTH - Static variable in class net.sf.basedb.core.data.UserData

The maximum length of the fax that can be stored in the database.

MAX_FAX_LENGTH - Static variable in class net.sf.basedb.core.User

The maximum length of the fax that can be stored in the database.

MAX_FORMAT_LENGTH - Static variable in class net.sf.basedb.core.data.FileServerData

MAX_FORMAT_LENGTH - Static variable in class net.sf.basedb.core.FileServer

The maximum length of the SSH private key format path that can be stored in the database.

MAX_FORMULA_LENGTH - Static variable in class net.sf.basedb.core.data.FormulaData

The maximum allowed length of a formula.

MAX_FORMULA_LENGTH - Static variable in class net.sf.basedb.core.Formula

The maximum length of the formula that can be stored in the database.

MAX_FROM_LENGTH - Static variable in class net.sf.basedb.core.data.MessageData

The maximum length of the from property.

MAX_FROM_LENGTH - Static variable in class net.sf.basedb.core.Message

The maximum length of the sender name.

MAX_HEADER_NAME_LENGTH - Static variable in class net.sf.basedb.core.data.RawBioAssayData

MAX_HEADER_NAME_LENGTH - Static variable in class net.sf.basedb.core.RawBioAssay

The maximum length of the name of a header that can be stored in the database.

MAX_HEADER_VALUE_LENGTH - Static variable in class net.sf.basedb.core.data.RawBioAssayData

MAX_HEADER_VALUE_LENGTH - Static variable in class net.sf.basedb.core.RawBioAssay

The maximum length of the value of a header that can be stored in the database.

MAX_HOST_LENGTH - Static variable in class net.sf.basedb.core.data.FileServerData

MAX_HOST_LENGTH - Static variable in class net.sf.basedb.core.FileServer

The maximum length of the host name:port that can be stored in the database.

MAX_IMAGE_LENGTH - Static variable in class net.sf.basedb.core.data.PlateMappingData

The maximum length of the image name that can be stored in the database.

MAX_IMAGE_LENGTH - Static variable in class net.sf.basedb.core.PlateMapping

The maximum length of the image name that can be stored in the database.

MAX_INFORMATION_LENGTH - Static variable in interface net.sf.basedb.core.plugin.About

The maximum length of the strings returned by the methods in this interface that can be stored in the database.

MAX_INTERFACENAME_LENGTH - Static variable in class net.sf.basedb.core.data.PluginTypeData

The maximum length of the interface name that can be stored in the database.

MAX_INTERFACENAME_LENGTH - Static variable in class net.sf.basedb.core.PluginType

The maximum length of the interface name that can be stored in the database.

MAX_ITEMS_IN_TRANSACTION - Static variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper

MAX_JARFILE_LENGTH - Static variable in class net.sf.basedb.core.data.PluginDefinitionData

MAX_JARFILE_LENGTH - Static variable in class net.sf.basedb.core.data.PluginTypeData

MAX_JARFILE_LENGTH - Static variable in class net.sf.basedb.core.PluginDefinition

The maximum length of the jar path name that can be stored in the database.

MAX_JARFILE_LENGTH - Static variable in class net.sf.basedb.core.PluginType

The maximum length of the jar path name that can be stored in the database.

MAX_LABEL_LENGTH - Static variable in class net.sf.basedb.core.data.ParameterValueData

The maximum length of the label of the parameter that can be stored in the database.

MAX_LAST_SOURCE_LENGTH - Static variable in class net.sf.basedb.core.data.ReporterData

The maximum length of the last source that can be stored in the database.

MAX_LOCATION_LENGTH - Static variable in class net.sf.basedb.core.data.SessionData

The maximum length of the location that can be stored in the database.

MAX_LOCATION_LENGTH - Static variable in class net.sf.basedb.core.data.UserDeviceData

The maximum length of the location that can be stored in the database.

MAX_LOGIN_COMMENT_LENGTH - Static variable in class net.sf.basedb.core.data.SessionData

The maximum length of the login comment that can be stored in the database.

MAX_LOGIN_LENGTH - Static variable in class net.sf.basedb.core.data.UserData

The maximum length of the login that can be stored in the database.

MAX_LOGIN_LENGTH - Static variable in class net.sf.basedb.core.User

The maximum length of the login that can be stored in the database.

MAX_MIMETYPE_LENGTH - Static variable in class net.sf.basedb.core.data.FileData

MAX_MIMETYPE_LENGTH - Static variable in class net.sf.basedb.core.File

The maximum length of the MIME type that can be stored in the database.

MAX_NAME_LENGTH - Static variable in class net.sf.basedb.core.data.ContextData

The maximum length of the name that can be stored in the database.

MAX_NAME_LENGTH - Static variable in interface net.sf.basedb.core.data.NameableData

The maximum length of the name of the item that can be stored in the database.

MAX_NAME_LENGTH - Static variable in class net.sf.basedb.core.data.PluginDefinitionData

The maximum length of the name that can be stored in the database.

MAX_NAME_LENGTH - Static variable in class net.sf.basedb.core.data.SettingData

The maximum length of the name of the setting that can be stored in the database.

MAX_NAME_LENGTH - Static variable in interface net.sf.basedb.core.Nameable

The maximum length of the name of the item that can be stored in the database.

MAX_NAME_LENGTH - Static variable in class net.sf.basedb.core.PluginDefinition

The maximum length of the name that can be stored in the database.

MAX_NAME_LENGTH - Static variable in class net.sf.basedb.core.Setting

The maximum length of the name that can be stored in the database.

MAX_NAME_LENGTH - Static variable in class net.sf.basedb.util.zip.TarUtil

Maximum file name length.

MAX_NEW_VALUE_LENGTH - Static variable in class net.sf.basedb.core.data.ChangeHistoryDetailData

MAX_OLD_VALUE_LENGTH - Static variable in class net.sf.basedb.core.data.ChangeHistoryDetailData

MAX_OPTION_LENGTH - Static variable in class net.sf.basedb.core.AnnotationType

The maximum length of an option.

MAX_OPTION_LENGTH - Static variable in class net.sf.basedb.core.data.AnnotationTypeData

MAX_ORGANISATION_LENGTH - Static variable in class net.sf.basedb.core.data.UserData

The maximum length of the organisation that can be stored in the database.

MAX_ORGANISATION_LENGTH - Static variable in class net.sf.basedb.core.User

The maximum length of the organisation that can be stored in the database.

MAX_PARENTS - Static variable in class net.sf.basedb.util.JarClassLoader

MAX_PASSWORD_LENGTH - Static variable in class net.sf.basedb.core.data.FileServerData

MAX_PASSWORD_LENGTH - Static variable in class net.sf.basedb.core.FileServer

The maximum length of the password that can be stored in the database.

MAX_PHONE_LENGTH - Static variable in class net.sf.basedb.core.data.UserData

The maximum length of the phone that can be stored in the database.

MAX_PHONE_LENGTH - Static variable in class net.sf.basedb.core.User

The maximum length of the phone that can be stored in the database.

MAX_PLUGIN_VERSION_LENGTH - Static variable in class net.sf.basedb.core.data.JobData

The maximum allowed length of the plugin version.

MAX_POSITION_LENGTH - Static variable in class net.sf.basedb.core.BioPlate

The maximum length of the position coordinate that can be stored in the database.

MAX_POSITION_LENGTH - Static variable in class net.sf.basedb.core.data.BioPlateData

The maximum length of the position coordinate that can be stored in the database.

MAX_PRIVATE_KEY_LENGTH - Static variable in class net.sf.basedb.core.data.FileServerData

MAX_PRIVATE_KEY_LENGTH - Static variable in class net.sf.basedb.core.FileServer

The maximum length of the SSH private key that can be stored in the database.

MAX_PUBLICATION_LENGTH - Static variable in class net.sf.basedb.core.data.ExperimentData

MAX_PUBLICATION_LENGTH - Static variable in class net.sf.basedb.core.Experiment

The maximum length of the publication property that can be stored in the database.

MAX_PUBMEDID_LENGTH - Static variable in class net.sf.basedb.core.data.ExperimentData

MAX_PUBMEDID_LENGTH - Static variable in class net.sf.basedb.core.Experiment

The maximum length of the pubMedId property that can be stored in the database.

MAX_RAWDATATYPE_LENGTH - Static variable in class net.sf.basedb.core.data.FormulaData

The maximum allowed length of the raw data type name.

MAX_REFERENCE_UNIT_LENGTH - Static variable in class net.sf.basedb.core.data.QuantityData

MAX_REFERENCE_UNIT_LENGTH - Static variable in class net.sf.basedb.core.Quantity

The maximum length of the reference unit that can be stored in the database.

MAX_REMOTE_ID_LENGTH - Static variable in class net.sf.basedb.core.data.SessionData

The maximum length of the remote ID that can be stored in the database.

MAX_REMOTE_ID_LENGTH - Static variable in class net.sf.basedb.core.data.UserDeviceData

The maximum length of the remote ID that can be stored in the database.

MAX_REPORT_LENGTH - Static variable in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyReportServlet

MAX_ROLE_LENGTH - Static variable in class net.sf.basedb.core.BioPlateEventParticipant

The maximum length of the role string that can be stored in the database.

MAX_ROLE_LENGTH - Static variable in class net.sf.basedb.core.data.BioPlateEventParticipantData

MAX_ROOT_PATH_LENGTH - Static variable in class net.sf.basedb.core.data.FileServerData

MAX_ROOT_PATH_LENGTH - Static variable in class net.sf.basedb.core.FileServer

The maximum length of the root path that can be stored in the database.

MAX_SECTION_LENGTH - Static variable in class net.sf.basedb.core.BioPlate

The maximum length of the section coordinate that can be stored in the database.

MAX_SECTION_LENGTH - Static variable in class net.sf.basedb.core.data.BioPlateData

The maximum length of the section coordinate that can be stored in the database.

MAX_SERVER_LENGTH - Static variable in class net.sf.basedb.core.data.JobAgentData

The maximum length of the server that can be stored in the database.

MAX_SERVER_LENGTH - Static variable in class net.sf.basedb.core.data.JobData

The maximum allowed length of the server name.

MAX_SERVER_LENGTH - Static variable in class net.sf.basedb.core.Job

The maximum allowed length of the server name.

MAX_SERVER_LENGTH - Static variable in class net.sf.basedb.core.JobAgent

The maximum length of the server name that can be stored in the database.

MAX_SIGNAL_TRANSPORTER_LENGTH - Static variable in class net.sf.basedb.core.data.JobData

The maximum allowed length of the signal transporter string.

MAX_SORTPROPERTY_LENGTH - Static variable in class net.sf.basedb.core.data.ContextData

The maximum length of the sort order that can be stored in the database.

MAX_STACK_TRACE_LENGTH - Static variable in class net.sf.basedb.core.data.JobData

The maximum allowed length of the stack trace message.

MAX_STACK_TRACE_LENGTH - Static variable in class net.sf.basedb.core.Job

The maximum allowed length of the stack trace message.

MAX_STATUS_MESSAGE_LENGTH - Static variable in class net.sf.basedb.core.data.JobData

The maximum allowed length of the status message.

MAX_STATUS_MESSAGE_LENGTH - Static variable in class net.sf.basedb.core.Job

The maximum allowed length of the status message.

MAX_SUBCONTEXT_LENGTH - Static variable in class net.sf.basedb.core.data.ContextData

The maximum length of the name that can be stored in the database.

MAX_SUBCONTEXT_LENGTH - Static variable in class net.sf.basedb.core.data.JobData

The maximum allowed length of the subcontext name.

MAX_SYMBOL_LENGTH - Static variable in class net.sf.basedb.core.data.ReporterData

The maximum length of the gene symbol that can be stored in the database.

MAX_SYMBOL_LENGTH - Static variable in class net.sf.basedb.core.data.UnitData

MAX_SYMBOL_LENGTH - Static variable in class net.sf.basedb.core.Unit

The maximum length of the display symbol that can be stored in the database.

MAX_SYSTEM_ID_LENGTH - Static variable in interface net.sf.basedb.core.data.SystemData

The maximum length of the system ID of the item that can be stored in the database.

MAX_SYSTEM_ID_LENGTH - Static variable in interface net.sf.basedb.core.SystemItem

The maximum length of the system ID that can be stored in the database.

MAX_TITLE_LENGTH - Static variable in class net.sf.basedb.core.data.ExperimentData

MAX_TITLE_LENGTH - Static variable in class net.sf.basedb.core.Experiment

The maximum length of the title property that can be stored in the database.

MAX_TOKEN_LENGTH - Static variable in class net.sf.basedb.core.data.UserDeviceData

The maximum length of the device token that can be stored in the database.

MAX_TRAY_LENGTH - Static variable in class net.sf.basedb.core.BioPlate

The maximum length of the tray coordinate that can be stored in the database.

MAX_TRAY_LENGTH - Static variable in class net.sf.basedb.core.data.BioPlateData

The maximum length of the tray coordinate that can be stored in the database.

MAX_URL_LENGTH - Static variable in class net.sf.basedb.clients.web.taglib.Page

MAX_URL_LENGTH - Static variable in class net.sf.basedb.core.data.FileData

MAX_URL_LENGTH - Static variable in class net.sf.basedb.core.data.PluginDefinitionData

The maximum length of the url that can be stored in the database.

MAX_URL_LENGTH - Static variable in class net.sf.basedb.core.data.UserData

The maximum length of the url that can be stored in the database.

MAX_URL_LENGTH - Static variable in class net.sf.basedb.core.File

The maximum length of the URL type that can be stored in the database.

MAX_URL_LENGTH - Static variable in class net.sf.basedb.core.PluginDefinition

The maximum length of the url that can be stored in the database.

MAX_URL_LENGTH - Static variable in class net.sf.basedb.core.User

The maximum length of the url that can be stored in the database.

MAX_USER_AGENT_LENGTH - Static variable in class net.sf.basedb.core.data.UserDeviceData

The maximum length of the user agent that can be stored in the database.

MAX_USERNAME_LENGTH - Static variable in class net.sf.basedb.core.data.FileServerData

MAX_USERNAME_LENGTH - Static variable in class net.sf.basedb.core.FileServer

The maximum length of the username that can be stored in the database.

MAX_VALUE - Static variable in enum class net.sf.basedb.core.Item

MAX_VALUE_LENGTH - Static variable in class net.sf.basedb.core.data.PropertyFilterData

The maximum length of the value that can be stored in the database.

MAX_VALUE_LENGTH - Static variable in class net.sf.basedb.core.data.SettingData

The maximum length of the value of the setting that can be stored in the database.

MAX_VALUE_LENGTH - Static variable in class net.sf.basedb.core.PropertyFilter

The maximum allowed length of a filter value.

MAX_VALUE_LENGTH - Static variable in class net.sf.basedb.core.Setting

The maximum length of the value that can be stored in the database.

MAX_VERSION_LENGTH - Static variable in class net.sf.basedb.core.data.PluginDefinitionData

The maximum length of the version that can be stored in the database.

MAX_VERSION_LENGTH - Static variable in class net.sf.basedb.core.PluginDefinition

The maximum length of the version that can be stored in the database.

MAX_VERSIONSTRING_LENGTH - Static variable in class net.sf.basedb.core.data.HardwareData

MAX_VERSIONSTRING_LENGTH - Static variable in class net.sf.basedb.core.data.SoftwareData

MAX_VERSIONSTRING_LENGTH - Static variable in class net.sf.basedb.core.Hardware

The maximum length of the version variable that can be stored in the database.

MAX_VERSIONSTRING_LENGTH - Static variable in class net.sf.basedb.core.Software

The maximum length of the version variable that can be stored in the database.

maxAge - Variable in class net.sf.basedb.core.DiskUsageStatistics

maxAge - Variable in class net.sf.basedb.util.OlderThanFileFilter

maxBaseVersion - Variable in class net.sf.basedb.core.plugin.AboutImpl

maxBaseVersion - Variable in class net.sf.basedb.util.extensions.AboutBean

maxBaseVersion - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredAbout

maxBytes - Variable in class net.sf.basedb.core.data.QuotaIndex

maxChannelsParameter - Variable in class net.sf.basedb.plugins.Base1PluginExecuter

The maximum number of channels, 0 means unlimited.

maxCharacters - Variable in class net.sf.basedb.clients.web.taglib.table.Cell

maxColor - Variable in class net.sf.basedb.util.ColorGenerator

maxDataColumns - Variable in class net.sf.basedb.util.parser.FlatFileParser

The maximun number of allowed data columns for a line to be considered a data line.

maxDataColumnsParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter

Parameter definition that asks for the maximum number of columns produced by the data splitter regexp for a line to be a data line.

maxDelay - Variable in class net.sf.basedb.util.TransferRateProgressReporter

maxEntries - Variable in class net.sf.basedb.util.extensions.logging.ExtensionsLog

MaxExpression - Class in net.sf.basedb.core.query

Calculates the maximum of an expression: MIN(e)

MaxExpression(Expression) - Constructor for class net.sf.basedb.core.query.MaxExpression

maxHeight - Variable in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet

maxHeight - Variable in class net.sf.basedb.clients.web.servlet.PlotServlet

maxHeight - Variable in class net.sf.basedb.clients.web.taglib.table.Cell

maxLength - Variable in class net.sf.basedb.core.StringParameterType

maxLength - Variable in class net.sf.basedb.util.parser.CropStringMapper

maxMemory - Variable in class net.sf.basedb.core.data.JobAgentSettingsData

maxMemory - Variable in class net.sf.basedb.core.data.PluginDefinitionData

maxParameters - Variable in class net.sf.basedb.core.FastAnnotationLoader.FastIterator

maxPosition - Variable in class net.sf.basedb.core.PositionBatcher

The maximum position number inserted by the batcher.

maxProjectPermission - Variable in class net.sf.basedb.core.Keyring

Holds the logged in user's maximum Permission within the active project.

maxRandomSamples - Variable in class net.sf.basedb.util.AnyToAnyLinkStatistics.Options

maxRawMappings - Variable in class net.sf.basedb.core.data.DataCubeData

maxResults - Variable in class net.sf.basedb.core.AbstractQuery

The maximum number of items that should be returned by the query.

maxSlots - Variable in class net.sf.basedb.clients.jobagent.slotmanager.InternalSlotManager

maxSlots - Variable in class net.sf.basedb.core.InternalJobQueue

The maximum number of threads that are allowed in each slot.

maxTicksPerSecond - Variable in class net.sf.basedb.util.TransferRateProgressReporter

maxUnknownLines - Variable in class net.sf.basedb.util.parser.FlatFileParser

The maximum number of unkown lines to parse before giving up.

maxValue - Variable in class net.sf.basedb.core.data.ColoringData

maxValue - Variable in class net.sf.basedb.util.ColorGenerator

maxValueColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

Column mapping parameter for "Max value".

maxValueMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

maxWidth - Variable in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet

maxWidth - Variable in class net.sf.basedb.clients.web.servlet.PlotServlet

maxWidth - Variable in class net.sf.basedb.clients.web.taglib.table.Cell

maybeEquals(Object) - Method in class net.sf.basedb.core.AnnotationRestriction

Check as many things as possible to try to determine if the other object is equal to this object.

maybeGranted - Variable in class net.sf.basedb.core.plugin.Permissions

maybeStopRunningJobs() - Method in class net.sf.basedb.clients.jobagent.Agent

Try to stop running jobs by interrupting the threads they are executing in.

MB - Static variable in class net.sf.basedb.util.Values

mColumn - Static variable in class net.sf.basedb.util.importer.spotdata.MAParser

md5 - Variable in class net.sf.basedb.core.data.FileData

md5 - Variable in class net.sf.basedb.core.data.ItemListSyncFilterData

md5 - Variable in class net.sf.basedb.core.File.UploadStream

The md5 sum calculater.

md5 - Variable in class net.sf.basedb.util.uri.UriMetadata

MD5 - Class in net.sf.basedb.util

This class calculates the MD5 hash of a string and returns it represented as a hexadecimal string.

MD5() - Constructor for class net.sf.basedb.util.MD5

MD5_FINGERPRINT_PATTERN - Static variable in class net.sf.basedb.core.FileServer

Pattern that matches a SSH MD5 fingerprint: 16 pairs of hexadecimal numbers separated with colon.

md5AtLastSync - Variable in class net.sf.basedb.core.data.ItemListData

mean - Variable in class net.sf.basedb.util.IntensityCalculatorUtil.JepIntensityCalculatorImpl

mean(String) - Method in class net.sf.basedb.util.jep.MeanFunction

Get the value of the specified property of the current raw data object.

mean(Expression) - Static method in class net.sf.basedb.core.query.Aggregations

Calculates the arithmetic mean of all values for an expression: new expression = AVG(e)

MEAN - Enum constant in enum class net.sf.basedb.util.plot.HistogramPlot.YAggregate

Plot the mean of all y-values for spots falling into each bin.

MeanExpression - Class in net.sf.basedb.core.query

Calculates the arithmetic mean of an expression: AVG(e)

MeanExpression(Expression) - Constructor for class net.sf.basedb.core.query.MeanExpression

MeanFunction - Class in net.sf.basedb.util.jep

A JEP function class that adds a mean(string) function to a JEP expression parser.

MeanFunction(DbControl) - Constructor for class net.sf.basedb.util.jep.MeanFunction

Create a new instance of this function working with raw data of the specified raw bio assay.

meanRawData(String) - Static method in class net.sf.basedb.core.query.Dynamic

Create an expression representing the mean value of a property of a raw data spot. expression = mean(rawdata.property).

MeanRawDataPropertyExpression - Class in net.sf.basedb.core

An expression representing the mean value of property of a raw data spot.

MeanRawDataPropertyExpression(String) - Constructor for class net.sf.basedb.core.MeanRawDataPropertyExpression

means - Variable in class net.sf.basedb.util.jep.MeanFunction

Holds a cache of the values.

MeasuredBioMaterial - Class in net.sf.basedb.core

This class is the base class for measured biomaterial items.

MeasuredBioMaterial(MeasuredBioMaterialData) - Constructor for class net.sf.basedb.core.MeasuredBioMaterial

MeasuredBioMaterial.RemainingQuantityAction - Class in net.sf.basedb.core

Transaction handler for updating the remaining quantity of a biomaterial based on the sum of the used quantity in this transaction.

MeasuredBioMaterialData - Class in net.sf.basedb.core.data

This class is the root class for measured biomaterials, ie biomaterials for where the quantity is tracked.

MeasuredBioMaterialData() - Constructor for class net.sf.basedb.core.data.MeasuredBioMaterialData

median(float[], int, int) - Method in class net.sf.basedb.plugins.MedianRatioNormalization

median(List<MedianRatioNormalization.SpotData>) - Method in class net.sf.basedb.plugins.MedianRatioNormalization

medianCorrection(List<LowessNormalization.SpotData>, Double[]) - Static method in class net.sf.basedb.plugins.LowessNormalization

MedianRatioNormalization - Class in net.sf.basedb.plugins

MedianRatioNormalization() - Constructor for class net.sf.basedb.plugins.MedianRatioNormalization

MedianRatioNormalization.SpotData - Class in net.sf.basedb.plugins

medianRatioSection - Static variable in class net.sf.basedb.plugins.MedianRatioNormalization

Section for normalization options

MEDIUM - Enum constant in enum class net.sf.basedb.core.Job.ExecutionTime

The job shouldn't take less than 1 hour to execute.

member - Variable in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext

member - Variable in class net.sf.basedb.util.fileset.ValidatingFileSetMember

member - Variable in class net.sf.basedb.util.overview.Fix

memberQuery - Variable in class net.sf.basedb.clients.web.formatter.DataFileFormatter

memberQuery - Variable in class net.sf.basedb.clients.web.plugins.FileSetMemberLoader

members - Variable in class net.sf.basedb.core.data.DataFileTypeData

members - Variable in class net.sf.basedb.core.data.FileSetData

members - Variable in class net.sf.basedb.core.data.ItemListData

members - Variable in class net.sf.basedb.util.fileset.ResetMetadataRenderer

members - Variable in class net.sf.basedb.util.fileset.ValidationRenderer

memberType - Variable in class net.sf.basedb.core.data.ItemListData

menu - Variable in class net.sf.basedb.clients.web.taglib.menu.Menuitem

The parent Menu.

menu - Variable in class net.sf.basedb.clients.web.taglib.menu.Menuseparator

menu - Variable in class net.sf.basedb.clients.web.taglib.menu.Submenu

The parent Menu.

menu - Variable in class net.sf.basedb.clients.web.taglib.Page

The name of the menu that should be displayed on the current page.

Menu - Class in net.sf.basedb.clients.web.taglib.menu

This tag defines a drop-down menu that is is opened when the user moves the mouse over or clicks at the title of the menu.

Menu() - Constructor for class net.sf.basedb.clients.web.taglib.menu.Menu

MENU - Static variable in class net.sf.basedb.clients.web.resources.Bundle

Resource bundle with string that are used in the menu.

menuId - Variable in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

menuId - Variable in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean

menuId - Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

Menuitem - Class in net.sf.basedb.clients.web.taglib.menu

This tag defines a menu item inside a drop-down menu.

Menuitem() - Constructor for class net.sf.basedb.clients.web.taglib.menu.Menuitem

MENUITEM - Enum constant in enum class net.sf.basedb.clients.web.extensions.menu.MenuItemAction.MenuType

This is a real menu item.

MenuItemAction - Interface in net.sf.basedb.clients.web.extensions.menu

An action for extensions to the menu system.

MenuItemAction.MenuType - Enum Class in net.sf.basedb.clients.web.extensions.menu

MenuItemBean - Class in net.sf.basedb.clients.web.extensions.menu

A simple bean-like implementation of the MenuItemAction interface.

MenuItemBean() - Constructor for class net.sf.basedb.clients.web.extensions.menu.MenuItemBean

Create a new empty menu item action.

Menuseparator - Class in net.sf.basedb.clients.web.taglib.menu

This tag defines a horizontal separator line inside a drop-down menu.

Menuseparator() - Constructor for class net.sf.basedb.clients.web.taglib.menu.Menuseparator

MenuType() - Constructor for enum class net.sf.basedb.clients.web.extensions.menu.MenuItemAction.MenuType

merge(Integer...) - Static method in enum class net.sf.basedb.core.Permission

Merges a list of integer permission values.

merge(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

merge(String, Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

merge(DbControl, ItemKey...) - Static method in class net.sf.basedb.core.ShareableUtil

Merge one or more item keys into a new item key that combines all the permissions.

merge(DbControl, ProjectKey...) - Static method in class net.sf.basedb.core.ShareableUtil

Merge one or more project keys into a new project key that combines all the permissions.

merge(ItemKey) - Method in class net.sf.basedb.core.GroupPermissions

Merge the permissions for all groups from the given item key with the permissions in this object.

merge(ItemKey) - Method in class net.sf.basedb.core.MultiPermissions

Merge the permissions from the given item key keeping those that has already been set.

merge(ItemKey) - Method in class net.sf.basedb.core.UserPermissions

Merge the permissions for all users from the given item key with the permissions in this object.

merge(EntityLogOptions) - Method in class net.sf.basedb.core.log.EntityLogOptions

Merge log options from the other object into this object.

merge(ProjectKey) - Method in class net.sf.basedb.core.MultiPermissions

Merge the permissions from the given project key keeping those that has already been set.

merge(ProjectKey) - Method in class net.sf.basedb.core.ProjectPermissions

Merge the permissions for all projects from the given project key with the permissions in this object.

mergeAnd(IdListRestriction) - Method in class net.sf.basedb.core.query.IdListRestriction

Merge this list with another list with AND logic respecting the notIn setting.

message - Variable in class net.sf.basedb.core.ItemContext

message - Variable in class net.sf.basedb.core.PluginResponse

message - Variable in class net.sf.basedb.core.signal.ExceptionInterruptHandler

message - Variable in class net.sf.basedb.core.SimpleAbsoluteProgressReporter

message - Variable in class net.sf.basedb.core.SimpleProgressReporter

message - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper

message - Variable in class net.sf.basedb.util.extensions.logging.LogEntry

message - Variable in class net.sf.basedb.util.fileset.ValidatingFileSetMember

message - Variable in class net.sf.basedb.util.fileset.ValidationRenderer

message - Variable in class net.sf.basedb.util.overview.Failure

message - Variable in class net.sf.basedb.util.overview.Fix

Message - Class in net.sf.basedb.core

This class represents a message.

Message(MessageData) - Constructor for class net.sf.basedb.core.Message

MESSAGE - Enum constant in enum class net.sf.basedb.core.Item

The item is a Message.

Message.QueryRuntimeFilterImpl - Class in net.sf.basedb.core

A runtime filter implementation that limits a query to only return messages for the currently logged in user unless the logged in user has generic read permission.

MessageData - Class in net.sf.basedb.core.data

This class holds information about messages.

MessageData() - Constructor for class net.sf.basedb.core.data.MessageData

messagePrefix - Variable in class net.sf.basedb.util.ChainedProgressReporter

messages - Variable in class net.sf.basedb.core.data.JobData

messages - Variable in class net.sf.basedb.core.data.UserData

messages - Variable in class net.sf.basedb.util.extensions.manager.ProcessResults.FileResults

MetaBlock(int) - Constructor for class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock

metaBlocks - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter

metaColumn - Variable in class net.sf.basedb.core.FeatureCoordinate

metadata - Variable in class net.sf.basedb.core.hibernate.DbIndexWork

metadata - Variable in class net.sf.basedb.core.hibernate.SchemaGenerator

metadata - Static variable in class net.sf.basedb.core.HibernateUtil

The mappings related to a configuration.

metadata - Variable in class net.sf.basedb.core.Metadata.EntityPropertyPath

metadata - Variable in class net.sf.basedb.util.export.spotdata.AssayPropertyField

metadata - Variable in class net.sf.basedb.util.uri.http.HttpConnectionManager

metaData - Variable in class net.sf.basedb.core.BasicBatcher

Hibernate metadata for the batchable object.

metaData - Static variable in class net.sf.basedb.core.Feature

metaData - Static variable in class net.sf.basedb.core.Reporter

metaData - Variable in class net.sf.basedb.util.jep.RawFunction

metaData - Variable in class net.sf.basedb.util.jep.ReporterFunction

Metadata<C> - Class in net.sf.basedb.core

Utility methods for retreiving metadata about items.

Metadata(Class<C>, String) - Constructor for class net.sf.basedb.core.Metadata

Metadata.BasicData2ItemPropertyPath<C extends BasicData,V extends BasicItem> - Class in net.sf.basedb.core

Property path implementation that converts a BasicData object to a BasicItem.

Metadata.BasicItem2DataPropertyPath<C extends BasicItem,V extends BasicData> - Class in net.sf.basedb.core

Property path implementation that converts a BasicItem to a BasicData object.

Metadata.CollectionPropertyPath<C> - Class in net.sf.basedb.core

Property path implementation which wraps a collection inside an unmodifiable collection.

Metadata.CombinedPropertyPath<C,V> - Class in net.sf.basedb.core

Property path implementation that combines a list of property paths to create a long chain.

Metadata.ComponentPropertyPath<C,V> - Class in net.sf.basedb.core

Property path implementation which gets a value from a component.

Metadata.DateCopyPropertyPath - Class in net.sf.basedb.core

Property path implementation clones a Date.

Metadata.EntityPropertyPath<C,V> - Class in net.sf.basedb.core

Property path implementation which gets a value from an entity.

Metadata.EvictPropertyPath<C> - Class in net.sf.basedb.core

Property path implementation that evicts the selected item from the Hibernate first-level cache.

Metadata.IdentifierPropertyPath - Class in net.sf.basedb.core

Property path implementation which gets the id from an entity.

Metadata.MapPropertyPath - Class in net.sf.basedb.core

Property path implementation which wraps a map inside an unmodifiable map.

Metadata.NoopPropertyPath<C> - Class in net.sf.basedb.core

Property path implementation that does nothing.

Metadata.PropertyPath<C,V> - Interface in net.sf.basedb.core

Contract for getting the value of a specific property for an item.

Metadata.ReporterScore2DataPropertyPath - Class in net.sf.basedb.core

Property path implementation that converts a ReporterScore to a ReporterListScoreData object.

MetadataModel - Class in net.sf.basedb.util.bfs

A model container of the contents of a BFS metadata file.

MetadataModel() - Constructor for class net.sf.basedb.util.bfs.MetadataModel

Create a new metadata model.

MetadataModel.Section - Class in net.sf.basedb.util.bfs

Holds information about a section.

MetadataModel.SectionEntry - Class in net.sf.basedb.util.bfs

Holds information about a section entry.

metadataParser - Variable in class net.sf.basedb.util.importer.spotdata.BfsImporter

MetadataParser - Class in net.sf.basedb.util.bfs

Parser implementation that parses a BFS metadata file.

MetadataParser() - Constructor for class net.sf.basedb.util.bfs.MetadataParser

Create a new metadata parser.

metadataPrefix - Variable in class net.sf.basedb.util.basefile.BaseFileWriter

metadataSources - Variable in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration

metadataWriter - Variable in class net.sf.basedb.util.export.spotdata.BfsExporter

MetadataWriter - Class in net.sf.basedb.util.bfs

Writer implementation for writing BFS metadata files.

MetadataWriter(Writer) - Constructor for class net.sf.basedb.util.bfs.MetadataWriter

Create a new BFS metadata writer.

metaGridX - Variable in class net.sf.basedb.core.BlockInfo

The X coordinate of the block.

metaGridX - Variable in class net.sf.basedb.core.data.ArrayDesignBlockData

metaGridX - Variable in class net.sf.basedb.core.data.RawData

metaGridX - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock

metaGridXColumnMapping - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

metaGridXColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

metaGridXMapper - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

metaGridXMapper - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

metaGridY - Variable in class net.sf.basedb.core.BlockInfo

The Y coordinate of the block.

metaGridY - Variable in class net.sf.basedb.core.data.ArrayDesignBlockData

metaGridY - Variable in class net.sf.basedb.core.data.RawData

metaGridY - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock

metaGridYColumnMapping - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

metaGridYColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

metaGridYMapper - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

metaGridYMapper - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

metaRow - Variable in class net.sf.basedb.core.FeatureCoordinate

method - Variable in class net.sf.basedb.core.authentication.AuthenticatedUser

method - Variable in class net.sf.basedb.core.authentication.AuthenticationMethod

method - Variable in class net.sf.basedb.plugins.batchimport.FallbackIdMethod

method - Variable in class net.sf.basedb.plugins.batchimport.InternalIdMethod

method - Variable in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod

method - Variable in class net.sf.basedb.plugins.batchimport.PropertyIdMethod

methods - Static variable in class net.sf.basedb.core.authentication.AuthenticationMethod

MEV_TDMS - Static variable in class net.sf.basedb.core.DataFileType

The external ID for the file type representing a MeV TDMS (Tab-Delimited Multiple Sample) file.

miameColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

Column mapping parameter for "Required for MIAME" flag.

miameMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

MICROARRAY_IMAGE - Static variable in class net.sf.basedb.core.DataFileType

The external ID for the file type representing scanned microarray image.

midColor - Variable in class net.sf.basedb.util.ColorGenerator

midValue - Variable in class net.sf.basedb.core.data.ColoringData

midValue - Variable in class net.sf.basedb.util.ColorGenerator

migrateAll(SessionControl, File, boolean, ProgressReporter) - Static method in class net.sf.basedb.core.MigrateRbaToDba

MigratedLogger() - Constructor for class net.sf.basedb.core.MigrateRbaToDba.MigratedLogger

MigrateRbaToDba - Class in net.sf.basedb.core

MigrateRbaToDba(DbControl, MigrateRbaToDba.SubtypeMapping, ProgressReporter) - Constructor for class net.sf.basedb.core.MigrateRbaToDba

MigrateRbaToDba.Itemlist - Class in net.sf.basedb.core

MigrateRbaToDba.LineMapping - Class in net.sf.basedb.core

MigrateRbaToDba.MigratedLogger - Class in net.sf.basedb.core

Used for adding log entries to the database if that is enabled.

MigrateRbaToDba.Rba - Class in net.sf.basedb.core

Hold information a raw bioassay.

MigrateRbaToDba.SubtypeMapping - Class in net.sf.basedb.core

Hold the mappings defined in the mapping file.

Migration - Class in net.sf.basedb.core

Class for migrating a database to PostgreSQL.

Migration(boolean, File, Session, ProgressReporter) - Constructor for class net.sf.basedb.core.Migration

Migration.ProgressInputStream - Class in net.sf.basedb.core

mimeType - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload.SectionHeaders

mimeType - Variable in class net.sf.basedb.clients.web.fileupload.UploadedFile

mimeType - Variable in class net.sf.basedb.core.data.FileData

mimeType - Variable in class net.sf.basedb.util.uri.UriMetadata

MimeType - Class in net.sf.basedb.core

This class is used to represent mime types.

MimeType(MimeTypeData) - Constructor for class net.sf.basedb.core.MimeType

Creates a new mimetype item from the given data.

MIMETYPE - Enum constant in enum class net.sf.basedb.core.Item

The item is a MimeType.

mimeTypeColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.FileImporter

MimeTypeData - Class in net.sf.basedb.core.data

This class holds information about mimetypes

MimeTypeData() - Constructor for class net.sf.basedb.core.data.MimeTypeData

mimeTypeMapper - Variable in class net.sf.basedb.plugins.batchimport.FileImporter

mimeTypes - Static variable in class net.sf.basedb.plugins.Bzip2FileUnpacker

mimeTypes - Static variable in class net.sf.basedb.plugins.GzipFileUnpacker

mimeTypes - Static variable in class net.sf.basedb.plugins.TarFileUnpacker

mimeTypes - Static variable in class net.sf.basedb.plugins.ZipFileUnpacker

min - Variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin

min(Expression) - Static method in class net.sf.basedb.core.query.Aggregations

Calculates the minimum value of an expression: new expression = MIN(e)

MIN - Enum constant in enum class net.sf.basedb.core.Formula.AverageMethod

MIN - Enum constant in enum class net.sf.basedb.util.plot.HistogramPlot.YAggregate

Plot the minimum of all y-values for spots falling into each bin.

minBaseVersion - Variable in class net.sf.basedb.core.plugin.AboutImpl

minBaseVersion - Variable in class net.sf.basedb.util.extensions.AboutBean

minBaseVersion - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredAbout

minChannelsParameter - Variable in class net.sf.basedb.plugins.Base1PluginExecuter

The minimum number of channels.

minColor - Variable in class net.sf.basedb.util.ColorGenerator

minCount - Variable in class net.sf.basedb.util.AnyToAnyLinkStatistics.Options

minDataColumns - Variable in class net.sf.basedb.util.parser.FlatFileParser

The minimun number of allowed data columns for a line to be considered a data line.

minDataColumnsParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter

Parameter definition that asks for the minimum number of columns produced by the data splitter regexp for a line to be a data line.

mIndex - Variable in class net.sf.basedb.util.importer.spotdata.MAParser

MINE - Enum constant in enum class net.sf.basedb.core.Include

Include item owned by the logged in user.

MinExpression - Class in net.sf.basedb.core.query

Calculates the minumum of an expression: MIN(e)

MinExpression(Expression) - Constructor for class net.sf.basedb.core.query.MinExpression

minFraction - Variable in class net.sf.basedb.util.AnyToAnyLinkStatistics.Options

minIntensityParameter - Variable in class net.sf.basedb.plugins.MedianRatioNormalization

minor - Static variable in class net.sf.basedb.core.Version

minValue - Variable in class net.sf.basedb.core.data.ColoringData

minValue - Variable in class net.sf.basedb.util.ColorGenerator

minValueColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

Column mapping parameter for "Min value".

minValueMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

missing(String, String) - Method in class net.sf.basedb.util.formatter.PropertyFilterFormatter

missing(String, String, Item, EntityQuery) - Static method in class net.sf.basedb.core.query.AnyToAnyRestriction

Create a restriction that restrict a query to return items that is missing a linked item with the given link name.

MISSING_ANYTOANY - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for a missing reference in an any-to-any link.

MISSING_ARRAYBATCH - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for missing array batch.

MISSING_ARRAYDESIGN - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for missing array design.

MISSING_ARRAYSLIDE - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for missing array slide.

MISSING_BIOPLATE - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for missing bioplate location.

MISSING_BIOSOURCE - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for missing biosource.

MISSING_DATAFILE - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if all files required by the platform are present or not.

MISSING_DERIVEDBIOASSAY - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for missing parent derived bioassay.

MISSING_EXTRACT - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for missing extract.

MISSING_FACTORVALUE - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for missing experimental factor value.

MISSING_FILE - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for denied access to (data) files.

MISSING_HARDWARE - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for missing hardware.

MISSING_KIT - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for missing kits.

MISSING_MIAME_ANNOTATION - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for missing "Required for MIAME" annotation.

MISSING_PARAMETER - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for missing protocol parameter values.

MISSING_PHYSICALBIOASSAY - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for missing physical bioassay.

MISSING_PROTOCOL - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for missing protocols.

MISSING_SAMPLE - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for missing sample.

MISSING_SOFTWARE - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for missing software.

MISSING_TAG - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks for missing tag.

missingReporterErrorParameter - Static variable in class net.sf.basedb.plugins.IlluminaRawDataImporter

missingReporterErrorParameter - Static variable in class net.sf.basedb.plugins.PlateFlatFileImporter

missingReporterErrorParameter - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

missingReporterErrorParameter - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

missingWellErrorParameter - Static variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter

mode - Variable in class net.sf.basedb.clients.web.formatter.DataFileFormatter

mode - Variable in class net.sf.basedb.clients.web.ModeInfo.ModeContext

mode - Variable in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget

mode - Variable in class net.sf.basedb.core.hibernate.SchemaGenerator

mode() - Method in class net.sf.basedb.clients.web.ModeInfo.ModeContext

Mode(boolean, boolean) - Constructor for enum class net.sf.basedb.core.hibernate.SchemaGenerator.Mode

ModeContext(Item, ModeInfo) - Constructor for class net.sf.basedb.clients.web.ModeInfo.ModeContext

ModeInfo - Class in net.sf.basedb.clients.web

ModeInfo(String, String, String, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, Permission, boolean) - Constructor for class net.sf.basedb.clients.web.ModeInfo

ModeInfo.ModeContext - Class in net.sf.basedb.clients.web

This implementation create main contextes from a mode and item type which means that we can have different default subcontexts for the default list pages and for selection list pages.

modes - Static variable in class net.sf.basedb.clients.web.ModeInfo

modified - Variable in class net.sf.basedb.core.hibernate.SchemaGenerator.SqlStatement

modified - Variable in class net.sf.basedb.core.SessionControl.SettingInfo

If the setting has been modified while the user was logged in or not

MOLAR_CONCENTRATION - Static variable in class net.sf.basedb.core.Quantity

The id for the Quantity object representing substance concentration.

MOMENTUM - Static variable in class net.sf.basedb.core.Quantity

The id for the Quantity object representing momentum.

moreAttributes - Variable in class net.sf.basedb.clients.web.extensions.DynamicActionAttributeSupport

MOVE - Static variable in class net.sf.basedb.core.BioPlateEventType

The system ID for "Move" event type.

MultiEventHandler - Class in net.sf.basedb.util.bfs

Event handler implementation that forwards a single event to multiple event handlers.

MultiEventHandler() - Constructor for class net.sf.basedb.util.bfs.MultiEventHandler

Create a new event handler.

MultiFormatter - Class in net.sf.basedb.util.formatter

A generic formatter that can be used to format objects of mixed classes.

MultiFormatter(Formatter<Object>, boolean) - Constructor for class net.sf.basedb.util.formatter.MultiFormatter

Create a new multi formatter.

MultiFormatter(Formatter<Object>, boolean, boolean) - Constructor for class net.sf.basedb.util.formatter.MultiFormatter

Create a new multi formatter.

multiHop - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

MultiPermissions - Class in net.sf.basedb.core

This is a helper class that is very useful when you have a collection of Shareable items and want to modify some permissions on all of them without affecting the rest of the permissions.

MultiPermissions(Collection<? extends SharedItem>) - Constructor for class net.sf.basedb.core.MultiPermissions

Create a new MultiPermissions object and feed it the collection of Shareable items that you want to modify.

multiple - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef

multiple - Variable in class net.sf.basedb.core.data.ItemSubtypeFileTypeData

multiple - Variable in class net.sf.basedb.core.data.PlatformFileTypeData

multiple - Variable in class net.sf.basedb.core.Install.ItemSubtypeFT

multiple - Variable in class net.sf.basedb.core.Install.PlatformFT

multiple - Variable in class net.sf.basedb.plugins.executor.ParameterDefinition

MULTIPLE_ARRAYDESIGNS - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if all raw bioassays in an experiment uses the same array design.

multipleItemsFoundErrorParameter - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

multipleItemsFoundErrorParameter - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

multipleItemsFoundErrorParameter - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

multiplePositionsError - Static variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter

multipleReferencesFoundErrorParameter - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

multipleTargetsFoundErrorParameter - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

multiplicity - Variable in class net.sf.basedb.core.data.AnnotationTypeData

multiplicity - Variable in class net.sf.basedb.core.ParameterType

How many values that can be tied to this parameter. 0 is unlimited values and 1 is default.

multiplicityColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

Column mapping parameter for annotation multiplicty.

multiplicityMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

multiply(Expression, Expression) - Static method in class net.sf.basedb.core.query.Expressions

Multiply two expressions: new expression = e1 * e2.

MultiplyConverter - Class in net.sf.basedb.util.jep.convert

Convert Multiply function to a Query API Expression.

MultiplyConverter() - Constructor for class net.sf.basedb.util.jep.convert.MultiplyConverter

MultiplyExpression - Class in net.sf.basedb.core.query

Multiply two expressions: e1 * e2.

MultiplyExpression(Expression, Expression) - Constructor for class net.sf.basedb.core.query.MultiplyExpression

MultiPropertyIdMethod - Class in net.sf.basedb.plugins.batchimport

Identification method implementation that can use a multiple properties (eg, name, id, externalId, etc.) for identifying items.

MultiPropertyIdMethod(String, String, String[], boolean, Type) - Constructor for class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod

Create a new id method.

MultiProtocolRequestHandler - Class in net.sf.basedb.clients.jobagent.handlers

Request handler implementation that forwards all requests to a registered protocol-specific handler.

MultiProtocolRequestHandler(Agent, RequestHandler) - Constructor for class net.sf.basedb.clients.jobagent.handlers.MultiProtocolRequestHandler

Create a new multi-protocol request handler.

MultiQueryIterator<E extends BasicItem> - Class in net.sf.basedb.util.query

Helper class for executing multiple queries and return the result as a single iterator.

MultiQueryIterator(DbControl, ItemQuery<? extends E>[]) - Constructor for class net.sf.basedb.util.query.MultiQueryIterator

MultiStepCollectionTransformer<S,D> - Class in net.sf.basedb.util.collections

Collection transformer implementation that transforms a source collection into the destination collection using multiple steps.

MultiStepCollectionTransformer(List<CollectionTransformer<?, ?>>) - Constructor for class net.sf.basedb.util.collections.MultiStepCollectionTransformer

MultiUpdateWork - Class in net.sf.basedb.core.hibernate

A JDBC Work implementation that executes multiple queries that doesn't return any result.

MultiUpdateWork(Collection<String>) - Constructor for class net.sf.basedb.core.hibernate.MultiUpdateWork

Create a new work item.

multiuserAccount - Variable in class net.sf.basedb.core.data.UserData

MWBR - Enum constant in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.FormatType

MySkinAction(FixedSkinActionFactory, String) - Constructor for class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory.MySkinAction

MySQLEngine - Class in net.sf.basedb.core.dbengine

Database engine for My SQL.

MySQLEngine() - Constructor for class net.sf.basedb.core.dbengine.MySQLEngine

Create MySQLEngine.

N

n - Variable in class net.sf.basedb.util.basefile.BaseFileWriter

name - Variable in class net.sf.basedb.clients.jobagent.Agent

name - Variable in class net.sf.basedb.clients.web.extensions.DynamicActionAttribute

name - Variable in class net.sf.basedb.clients.web.extensions.ServletWrapper

name - Variable in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory

name - Variable in class net.sf.basedb.clients.web.extensions.startpage.StartPageBean

name - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload.SectionHeaders

name - Variable in class net.sf.basedb.clients.web.ModeInfo

name - Variable in class net.sf.basedb.clients.web.plugins.ExportedProperty

name - Variable in class net.sf.basedb.clients.web.SubContext

name - Variable in class net.sf.basedb.clients.web.taglib.Input

The name of the input element.

name - Variable in class net.sf.basedb.clients.web.taglib.table.Hidden

The name of the element.

name - Variable in class net.sf.basedb.core.authentication.ExtraUserInformation

name - Variable in class net.sf.basedb.core.BatchedPropertyInfo

name - Variable in class net.sf.basedb.core.data.AnyToAnyData

name - Variable in class net.sf.basedb.core.data.BioAssayData

name - Variable in class net.sf.basedb.core.data.BioAssaySetData

name - Variable in class net.sf.basedb.core.data.BioPlateEventTypeData

name - Variable in class net.sf.basedb.core.data.BioPlateTypeData

name - Variable in class net.sf.basedb.core.data.ChangeHistoryData

name - Variable in class net.sf.basedb.core.data.CommonData

name - Variable in class net.sf.basedb.core.data.ContextData

name - Variable in class net.sf.basedb.core.data.ContextIndex

name - Variable in class net.sf.basedb.core.data.DataFileTypeData

name - Variable in class net.sf.basedb.core.data.ExtraValueTypeData

name - Variable in class net.sf.basedb.core.data.GroupData

name - Variable in class net.sf.basedb.core.data.HelpData

name - Variable in class net.sf.basedb.core.data.ItemListSyncFilterData

name - Variable in class net.sf.basedb.core.data.ItemSubtypeData

name - Variable in class net.sf.basedb.core.data.MessageData

name - Variable in class net.sf.basedb.core.data.MimeTypeData

name - Variable in class net.sf.basedb.core.data.NewsData

name - Variable in class net.sf.basedb.core.data.PlateEventTypeData

name - Variable in class net.sf.basedb.core.data.PlateGeometryData

name - Variable in class net.sf.basedb.core.data.PlatformData

name - Variable in class net.sf.basedb.core.data.PlatformVariantData

name - Variable in class net.sf.basedb.core.data.PluginDefinitionData

name - Variable in class net.sf.basedb.core.data.PluginTypeData

name - Variable in class net.sf.basedb.core.data.ProjectData

name - Variable in class net.sf.basedb.core.data.QuantityData

name - Variable in class net.sf.basedb.core.data.QuotaData

name - Variable in class net.sf.basedb.core.data.QuotaTypeData

name - Variable in class net.sf.basedb.core.data.ReporterData

name - Variable in class net.sf.basedb.core.data.ReporterTypeData

name - Variable in class net.sf.basedb.core.data.RoleData

name - Variable in class net.sf.basedb.core.data.RoleKeyData

name - Variable in class net.sf.basedb.core.data.RootRawBioAssayData

name - Variable in class net.sf.basedb.core.data.SettingData

name - Variable in class net.sf.basedb.core.data.TransformationData

name - Variable in class net.sf.basedb.core.data.UnitData

name - Variable in class net.sf.basedb.core.data.UserData

name - Variable in class net.sf.basedb.core.data.UserDeviceData

name - Variable in class net.sf.basedb.core.data.VersionedParameter

The name of the parameter.

name - Variable in class net.sf.basedb.core.DbControl

The name of this transaction.

name - Variable in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo

name - Variable in class net.sf.basedb.core.dbengine.TableInfo.ForeignKeyInfo

name - Variable in class net.sf.basedb.core.dbengine.TableInfo.IndexInfo

name - Variable in class net.sf.basedb.core.dbengine.TableInfo.PrimaryKeyInfo

name - Variable in class net.sf.basedb.core.ExtendedProperty

name - Variable in class net.sf.basedb.core.HibernateUtil.DelayedFilterDef

name - Variable in class net.sf.basedb.core.IntensityFormula

name - Variable in class net.sf.basedb.core.ItemContext

name - Variable in class net.sf.basedb.core.LogControl

name - Variable in class net.sf.basedb.core.MigrateRbaToDba.Itemlist

name - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba

name - Variable in class net.sf.basedb.core.plugin.AboutImpl

name - Variable in class net.sf.basedb.core.PluginParameter

The name of the parameter that the plugin use to identify the value with.

name - Variable in class net.sf.basedb.core.Presets.Preset

The name of this preset.

name - Variable in class net.sf.basedb.core.query.HqlEntityParameterExpression

name - Variable in class net.sf.basedb.core.query.ParameterExpression

name - Variable in class net.sf.basedb.core.query.QueryParameter

name - Variable in class net.sf.basedb.core.RawDataType

name - Variable in class net.sf.basedb.core.SessionControl.ClientInfo

name - Variable in class net.sf.basedb.core.signal.Signal

name - Variable in class net.sf.basedb.core.VirtualColumn

The name of the column.

name - Variable in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter

name - Variable in class net.sf.basedb.plugins.executor.ParameterDefinition

name - Variable in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section

name - Variable in class net.sf.basedb.util.bfs.MetadataModel.Section

name - Variable in class net.sf.basedb.util.excel.XlsxTableWriter

name - Variable in class net.sf.basedb.util.extensions.AboutBean

name - Variable in class net.sf.basedb.util.extensions.events.EventType

name - Variable in class net.sf.basedb.util.extensions.ExtensionPointBean

name - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile

name - Variable in class net.sf.basedb.util.extensions.Registry.AttributeKey

name - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredAbout

name - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint

name - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay

name - Variable in class net.sf.basedb.util.jep.FunctionSafeJep.UnknownFunction

name - Variable in class net.sf.basedb.util.jep.SimpleJepFunction

name - Variable in class net.sf.basedb.util.overview.Node

name - Variable in class net.sf.basedb.util.parser.ColumnMapper

name - Variable in class net.sf.basedb.util.parser.FlatFileParser.Line

name - Variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramSeries

name - Variable in class net.sf.basedb.util.plot.HistogramPlot.TempSeries

name - Variable in class net.sf.basedb.util.plot.PlotAnnotation

name - Variable in class net.sf.basedb.util.resources.ResourceBundleWrapper

name - Variable in class net.sf.basedb.util.uri.http.HttpConnectionManagerFactory

name() - Method in class net.sf.basedb.util.parser.FlatFileParser.Line

The name of the header if the line is a header line.

name(String) - Method in class net.sf.basedb.util.formatter.PropertyFilterFormatter

NAME - Static variable in class net.sf.basedb.core.ClonableProperty

The property name of the "static" property ReporterData.getName()

NAME - Static variable in class net.sf.basedb.plugins.batchimport.PropertyIdMethod

Use the name for finding items.

NAME_COMPARATOR - Static variable in class net.sf.basedb.util.extensions.xml.PluginInfo

Comparator that sort plug-ins according to their names.

NAME_OR_BARCODE - Static variable in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod

Use the name or barcode for finding items.

NAME_OR_BARCODE_OR_ID - Static variable in class net.sf.basedb.plugins.batchimport.FallbackIdMethod

NAME_OR_EXTERNALID - Static variable in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod

Use the name or external ID for finding items.

NAME_OR_EXTERNALID_OR_ID - Static variable in class net.sf.basedb.plugins.batchimport.FallbackIdMethod

NAME_OR_ID - Static variable in class net.sf.basedb.plugins.batchimport.FallbackIdMethod

Use the name for finding items.

NAME_OR_SYSTEMID - Static variable in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod

Use the name or system Id for finding items.

NAME_OR_SYSTEMID_OR_ID - Static variable in class net.sf.basedb.plugins.batchimport.FallbackIdMethod

Use the name or system ID for finding items.

NAME_OR_UNITSYMBOL - Static variable in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod

Use the name or unit symbol for finding items.

NAME_OR_UNITSYMBOL_OR_ID - Static variable in class net.sf.basedb.plugins.batchimport.FallbackIdMethod

ID method that can be used for units.

NAME_PATTERN - Static variable in class net.sf.basedb.clients.web.fileupload.FileUpload

Nameable - Interface in net.sf.basedb.core

A Nameable item is an item that has a name and description.

NameableComparator<T extends Nameable> - Class in net.sf.basedb.util

An implementation of the Comparator interface which uses the name of Nameable items to compare the objects.

NameableComparator(boolean) - Constructor for class net.sf.basedb.util.NameableComparator

Create a new comparator.

NameableConverter<T extends Nameable> - Class in net.sf.basedb.util.json

Simple "converter" implementation that create JSON objects with the name and id of Nameable items.

NameableConverter() - Constructor for class net.sf.basedb.util.json.NameableConverter

NameableData - Interface in net.sf.basedb.core.data

A nameable item is an item that has a name and, optionally, a description.

NameableFormatter - Class in net.sf.basedb.util.formatter

Formatter to handle Nameable items.

NameableFormatter() - Constructor for class net.sf.basedb.util.formatter.NameableFormatter

Create a new formatter.

NameableFormatter(String) - Constructor for class net.sf.basedb.util.formatter.NameableFormatter

Create a new formatter.

nameableItems - Static variable in class net.sf.basedb.core.Metadata

NameableNameGenerator<I extends Nameable> - Class in net.sf.basedb.util.overview.node

Name generator implementation for Nameable items.

NameableNameGenerator(String, String) - Constructor for class net.sf.basedb.util.overview.node.NameableNameGenerator

Create a new name generator.

NameableNodeValidator<I extends Nameable> - Class in net.sf.basedb.util.overview.validator

NameableNodeValidator(Validator, Validator) - Constructor for class net.sf.basedb.util.overview.validator.NameableNodeValidator

Creates a new validator.

NameableUtil - Class in net.sf.basedb.core

Utility methods that will make it easier to implement the Nameable interface, including data validation.

NameableUtil() - Constructor for class net.sf.basedb.core.NameableUtil

nameColumnMapping - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

nameColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

nameColumnMapping - Static variable in class net.sf.basedb.plugins.PlateFlatFileImporter

nameColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

NameComparator() - Constructor for class net.sf.basedb.core.RawDataTypes.NameComparator

namedCubes - Variable in class net.sf.basedb.core.Transformation

Internal cache of named cubes used by the newProduct method.

namedFormulas - Variable in class net.sf.basedb.core.RawDataType

namedLayers - Variable in class net.sf.basedb.core.Transformation

Internal cache of named layers used by the newProduct method.

namedParameter - Static variable in class net.sf.basedb.core.AbstractSqlQuery

Pattern that finds a named parameter in an SQL string.

namedProperties - Variable in class net.sf.basedb.core.RawDataType

nameGenerator - Variable in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader

nameGenerator - Variable in class net.sf.basedb.util.overview.node.NodeFactory

nameMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

nameMapper - Variable in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter

nameMapper - Variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter

nameMapper - Variable in class net.sf.basedb.plugins.batchimport.ArraySlideImporter

nameMapper - Variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter

nameMapper - Variable in class net.sf.basedb.plugins.batchimport.BioSourceImporter

nameMapper - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

nameMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter

nameMapper - Variable in class net.sf.basedb.plugins.batchimport.KitImporter

nameMapper - Variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter

nameMapper - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

nameMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter

nameMapper - Variable in class net.sf.basedb.plugins.batchimport.TagImporter

nameMapper - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter

nameMapper - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

nameOfItem(DbControl, Item, int, boolean) - Method in class net.sf.basedb.util.formatter.PropertyFilterFormatter

namePaddingParameter - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter

nameParameter - Static variable in class net.sf.basedb.plugins.IntensityCalculatorPlugin

nameParameter - Static variable in class net.sf.basedb.plugins.PlateMappingImporter

namePrefix - Variable in class net.sf.basedb.util.overview.node.NameableNameGenerator

names - Variable in class net.sf.basedb.util.timer.PerformanceTimer

namespace - Static variable in class net.sf.basedb.clients.web.extensions.ServletLoader

The name of the servlets namespace.

namespace - Variable in class net.sf.basedb.core.plugin.NamespaceParameterValuesWrapper

namespace - Variable in class net.sf.basedb.core.plugin.NamespaceRequestWrapper

NAMESPACE - Static variable in class net.sf.basedb.util.extensions.xml.XmlLoader

The name of the extensions namespace.

NAMESPACE_EXPORTER - Static variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

The namespace for the exporter plug-in parameters.

NAMESPACE_EXTERNAL - Static variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

The namespace for the external program parameters.

NAMESPACE_IMPORTER - Static variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

The namespace for the importer plug-in parameters.

NamespaceParameterValuesWrapper - Class in net.sf.basedb.core.plugin

A helper class that wraps a parameter values object with a namespace.

NamespaceParameterValuesWrapper(ParameterValues, String) - Constructor for class net.sf.basedb.core.plugin.NamespaceParameterValuesWrapper

Create a new namespace wrapper for the parent parameter values.

NamespacePluginParameter<T> - Class in net.sf.basedb.core.plugin

A helper class that wraps a plug-in parameter object with a namespace.

NamespacePluginParameter(PluginParameter<T>, String) - Constructor for class net.sf.basedb.core.plugin.NamespacePluginParameter

Create a new parameter wrapper for the plug-in parameter.

NamespaceRequestWrapper - Class in net.sf.basedb.core.plugin

A helper class that wraps a request object with a namespace.

NamespaceRequestWrapper(Request, String) - Constructor for class net.sf.basedb.core.plugin.NamespaceRequestWrapper

Create a new namespace wrapper for the parent request.

nameTemplate - Variable in enum class net.sf.basedb.core.VirtualTable

The name template, # is replaced by the ID of the VirtualDb item.

nameType - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

A parameter type for name parameters which are required and must have a value.

nameType - Static variable in class net.sf.basedb.plugins.IntensityCalculatorPlugin

NativeQueryWrapper<R> - Class in net.sf.basedb.core.hibernate

A simple wrapper around hibernate native (SQL) queries which simply forwards all calls to a parent query.

NativeQueryWrapper(NativeQuery<R>) - Constructor for class net.sf.basedb.core.hibernate.NativeQueryWrapper

NativeSQLFunction - Class in net.sf.basedb.core.hibernate

Helper class for mixing native SQL with HQL queries.

NativeSQLFunction() - Constructor for class net.sf.basedb.core.hibernate.NativeSQLFunction

NaturalLogarithmConverter - Class in net.sf.basedb.util.jep.convert

Convert NaturalLogarithm function to a Query API Expression.

NaturalLogarithmConverter() - Constructor for class net.sf.basedb.util.jep.convert.NaturalLogarithmConverter

Navigator - Class in net.sf.basedb.clients.web.taglib.table

This tag is used to display a navigator for a pageable table of items.

Navigator() - Constructor for class net.sf.basedb.clients.web.taglib.table.Navigator

NBSP - Static variable in class net.sf.basedb.util.formatter.PrefixSuffixFormatter

The character representing a non-breaking space.

needNewLine - Variable in class net.sf.basedb.util.ConsoleProgressReporter

needResourcesPerExtension - Variable in class net.sf.basedb.clients.web.extensions.JspContext

needSynchronize - Variable in class net.sf.basedb.core.BioPlateEvent

needToParseDate - Variable in class net.sf.basedb.util.parser.ConstantMapper

needToParseNumeric - Variable in class net.sf.basedb.util.parser.ConstantMapper

needWrapper - Variable in class net.sf.basedb.util.listable.CollectExtracts

negate(Expression) - Static method in class net.sf.basedb.core.query.Expressions

Negate an expression: new expression = -e1.

NegateExpression - Class in net.sf.basedb.core.query

Negate an expression: -e1.

NegateExpression(Expression) - Constructor for class net.sf.basedb.core.query.NegateExpression

neq(Expression, Expression) - Static method in class net.sf.basedb.core.query.Restrictions

Compare if two expressions are inequal: new restriction = e1 <> e2.

NEQ - Enum constant in enum class net.sf.basedb.core.Operator

NeqRestriction - Class in net.sf.basedb.core.query

Compare if two expressions are inequal: e1 <> e2, or NOT e1 IS NULL

NeqRestriction(Expression, Expression) - Constructor for class net.sf.basedb.core.query.NeqRestriction

NestedIterator<E> - Class in net.sf.basedb.util

This class implements the Iterator interface for iterating multiple collections as if it was one big collection.

NestedIterator(Collection<? extends E>...) - Constructor for class net.sf.basedb.util.NestedIterator

Create a new ArrayIterator object.

net.sf.basedb.clients.jobagent - package net.sf.basedb.clients.jobagent

net.sf.basedb.clients.jobagent.executors - package net.sf.basedb.clients.jobagent.executors

net.sf.basedb.clients.jobagent.handlers - package net.sf.basedb.clients.jobagent.handlers

net.sf.basedb.clients.jobagent.slotmanager - package net.sf.basedb.clients.jobagent.slotmanager

net.sf.basedb.clients.web - package net.sf.basedb.clients.web

net.sf.basedb.clients.web.extensions - package net.sf.basedb.clients.web.extensions

net.sf.basedb.clients.web.extensions.edit - package net.sf.basedb.clients.web.extensions.edit

net.sf.basedb.clients.web.extensions.fileviewer - package net.sf.basedb.clients.web.extensions.fileviewer

net.sf.basedb.clients.web.extensions.list - package net.sf.basedb.clients.web.extensions.list

net.sf.basedb.clients.web.extensions.login - package net.sf.basedb.clients.web.extensions.login

net.sf.basedb.clients.web.extensions.menu - package net.sf.basedb.clients.web.extensions.menu

net.sf.basedb.clients.web.extensions.plot - package net.sf.basedb.clients.web.extensions.plot

net.sf.basedb.clients.web.extensions.renderer - package net.sf.basedb.clients.web.extensions.renderer

net.sf.basedb.clients.web.extensions.section - package net.sf.basedb.clients.web.extensions.section

net.sf.basedb.clients.web.extensions.service - package net.sf.basedb.clients.web.extensions.service

net.sf.basedb.clients.web.extensions.skin - package net.sf.basedb.clients.web.extensions.skin

net.sf.basedb.clients.web.extensions.startpage - package net.sf.basedb.clients.web.extensions.startpage

net.sf.basedb.clients.web.extensions.tabcontrol - package net.sf.basedb.clients.web.extensions.tabcontrol

net.sf.basedb.clients.web.extensions.toolbar - package net.sf.basedb.clients.web.extensions.toolbar

net.sf.basedb.clients.web.fileupload - package net.sf.basedb.clients.web.fileupload

This package contains classes for handling file uploads from a browser using the standard described in RFC1867.

net.sf.basedb.clients.web.formatter - package net.sf.basedb.clients.web.formatter

net.sf.basedb.clients.web.plugins - package net.sf.basedb.clients.web.plugins

net.sf.basedb.clients.web.resources - package net.sf.basedb.clients.web.resources

net.sf.basedb.clients.web.servlet - package net.sf.basedb.clients.web.servlet

net.sf.basedb.clients.web.taglib - package net.sf.basedb.clients.web.taglib

net.sf.basedb.clients.web.taglib.extensions - package net.sf.basedb.clients.web.taglib.extensions

net.sf.basedb.clients.web.taglib.menu - package net.sf.basedb.clients.web.taglib.menu

This package is a taglib that can be used on JSP pages to build a simple drop-down menu system with unlimited levels.

net.sf.basedb.clients.web.taglib.path - package net.sf.basedb.clients.web.taglib.path

net.sf.basedb.clients.web.taglib.tab - package net.sf.basedb.clients.web.taglib.tab

net.sf.basedb.clients.web.taglib.table - package net.sf.basedb.clients.web.taglib.table

net.sf.basedb.clients.web.util - package net.sf.basedb.clients.web.util

net.sf.basedb.core - package net.sf.basedb.core

This package contains the core business logic of BASE.

net.sf.basedb.core.authentication - package net.sf.basedb.core.authentication

net.sf.basedb.core.data - package net.sf.basedb.core.data

This package contains pure data-holder classes which are mapped to the database using Hibernate.

net.sf.basedb.core.data.annotations - package net.sf.basedb.core.data.annotations

net.sf.basedb.core.data.keyring - package net.sf.basedb.core.data.keyring

This package contains helper classes for the Keyring class.

net.sf.basedb.core.dbengine - package net.sf.basedb.core.dbengine

net.sf.basedb.core.hibernate - package net.sf.basedb.core.hibernate

net.sf.basedb.core.log - package net.sf.basedb.core.log

net.sf.basedb.core.log.db - package net.sf.basedb.core.log.db

net.sf.basedb.core.migrate - package net.sf.basedb.core.migrate

net.sf.basedb.core.migrate.postgres - package net.sf.basedb.core.migrate.postgres

net.sf.basedb.core.plugin - package net.sf.basedb.core.plugin

net.sf.basedb.core.query - package net.sf.basedb.core.query

This package contains the core of the Query API.

net.sf.basedb.core.signal - package net.sf.basedb.core.signal

net.sf.basedb.core.snapshot - package net.sf.basedb.core.snapshot

net.sf.basedb.plugins - package net.sf.basedb.plugins

net.sf.basedb.plugins.batchimport - package net.sf.basedb.plugins.batchimport

net.sf.basedb.plugins.executor - package net.sf.basedb.plugins.executor

net.sf.basedb.plugins.gtf - package net.sf.basedb.plugins.gtf

net.sf.basedb.plugins.util - package net.sf.basedb.plugins.util

net.sf.basedb.util - package net.sf.basedb.util

This package contains some useful utility classes and methods.

net.sf.basedb.util.affymetrix - package net.sf.basedb.util.affymetrix

net.sf.basedb.util.annotations - package net.sf.basedb.util.annotations

net.sf.basedb.util.basefile - package net.sf.basedb.util.basefile

net.sf.basedb.util.bcrypt - package net.sf.basedb.util.bcrypt

net.sf.basedb.util.bfs - package net.sf.basedb.util.bfs

net.sf.basedb.util.charset - package net.sf.basedb.util.charset

net.sf.basedb.util.collections - package net.sf.basedb.util.collections

net.sf.basedb.util.encode - package net.sf.basedb.util.encode

net.sf.basedb.util.error - package net.sf.basedb.util.error

net.sf.basedb.util.excel - package net.sf.basedb.util.excel

net.sf.basedb.util.export - package net.sf.basedb.util.export

net.sf.basedb.util.export.spotdata - package net.sf.basedb.util.export.spotdata

net.sf.basedb.util.extensions - package net.sf.basedb.util.extensions

net.sf.basedb.util.extensions.debug - package net.sf.basedb.util.extensions.debug

net.sf.basedb.util.extensions.events - package net.sf.basedb.util.extensions.events

net.sf.basedb.util.extensions.logging - package net.sf.basedb.util.extensions.logging

net.sf.basedb.util.extensions.manager - package net.sf.basedb.util.extensions.manager

net.sf.basedb.util.extensions.manager.filter - package net.sf.basedb.util.extensions.manager.filter

net.sf.basedb.util.extensions.manager.processor - package net.sf.basedb.util.extensions.manager.processor

net.sf.basedb.util.extensions.xml - package net.sf.basedb.util.extensions.xml

net.sf.basedb.util.fileset - package net.sf.basedb.util.fileset

net.sf.basedb.util.filter - package net.sf.basedb.util.filter

net.sf.basedb.util.formatter - package net.sf.basedb.util.formatter

net.sf.basedb.util.fuzzy - package net.sf.basedb.util.fuzzy

net.sf.basedb.util.gtf - package net.sf.basedb.util.gtf

net.sf.basedb.util.importer - package net.sf.basedb.util.importer

net.sf.basedb.util.importer.spotdata - package net.sf.basedb.util.importer.spotdata

net.sf.basedb.util.jep - package net.sf.basedb.util.jep

net.sf.basedb.util.jep.convert - package net.sf.basedb.util.jep.convert

net.sf.basedb.util.jobagent - package net.sf.basedb.util.jobagent

net.sf.basedb.util.json - package net.sf.basedb.util.json

net.sf.basedb.util.listable - package net.sf.basedb.util.listable

net.sf.basedb.util.ma - package net.sf.basedb.util.ma

net.sf.basedb.util.overview - package net.sf.basedb.util.overview

net.sf.basedb.util.overview.cache - package net.sf.basedb.util.overview.cache

net.sf.basedb.util.overview.extensions - package net.sf.basedb.util.overview.extensions

net.sf.basedb.util.overview.filter - package net.sf.basedb.util.overview.filter

net.sf.basedb.util.overview.loader - package net.sf.basedb.util.overview.loader

net.sf.basedb.util.overview.node - package net.sf.basedb.util.overview.node

net.sf.basedb.util.overview.validator - package net.sf.basedb.util.overview.validator

net.sf.basedb.util.parser - package net.sf.basedb.util.parser

net.sf.basedb.util.plot - package net.sf.basedb.util.plot

net.sf.basedb.util.query - package net.sf.basedb.util.query

net.sf.basedb.util.resources - package net.sf.basedb.util.resources

net.sf.basedb.util.ssl - package net.sf.basedb.util.ssl

net.sf.basedb.util.timer - package net.sf.basedb.util.timer

net.sf.basedb.util.transform - package net.sf.basedb.util.transform

net.sf.basedb.util.units - package net.sf.basedb.util.units

net.sf.basedb.util.uri - package net.sf.basedb.util.uri

net.sf.basedb.util.uri.http - package net.sf.basedb.util.uri.http

net.sf.basedb.util.zip - package net.sf.basedb.util.zip

NEW_SCHEMA_VERSION - Static variable in class net.sf.basedb.core.Install

The schema version to give to new installations.

NewAnnotations(Annotatable) - Constructor for class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations

Create a new cache for the specified item.

newArrayBatch() - Method in class net.sf.basedb.core.ArrayDesign

Create a new ArrayBatch with this design.

newArraySlide() - Method in class net.sf.basedb.core.ArrayBatch

Create a new ArraySlide item for this batch.

newBioAssay(Collection<BioAssay>) - Method in class net.sf.basedb.core.BioAssaySet

Create a new BioAssay with links to multiple parent bioassays.

newBioAssay(BioAssay) - Method in class net.sf.basedb.core.BioAssaySet

Create a new BioAssay in this bioassayset using a single parent.

newBioAssay(DataCubeColumn, Collection<BioAssay>) - Method in class net.sf.basedb.core.BioAssaySet

Create a new bioassay and link to the parents.

newBundle(String, Locale, String, ClassLoader, boolean) - Method in class net.sf.basedb.util.resources.Utf8PropertiesResourceBundleControl

Load property files using UTF-8.

newCh1 - Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData

newCh2 - Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData

newChildren - Variable in class net.sf.basedb.util.overview.Node

newClientSetting(Client, String, String) - Method in class net.sf.basedb.core.User

Create a new client application setting for this user.

newColumn() - Method in class net.sf.basedb.core.DataCube

Create a new column in this database.

newDataCube() - Method in class net.sf.basedb.core.VirtualDb

Create a new data cube in this virtual database.

newDbControl() - Method in class net.sf.basedb.core.SessionControl

Create a new DbControl object for this session.

newDbControl(String) - Method in class net.sf.basedb.core.SessionControl

Create a new name DbControl object for this session.

newDefaultSetting(String, String) - Method in class net.sf.basedb.core.Client

Create a new default setting for this client.

newDefaultSetting(String, String) - Method in class net.sf.basedb.core.User

Create a new default setting for this user.

newDynamicMapping(VirtualDb, VirtualTable, boolean) - Static method in class net.sf.basedb.core.HibernateUtil

Create a new org.hibernate.mapping.Table object for the specified table.

newEvent() - Method in class net.sf.basedb.core.MeasuredBioMaterial

Create a new event for this biomaterial.

newEvent(BioPlateEventParticipant) - Method in class net.sf.basedb.core.MeasuredBioMaterial

Create a new event for this biomaterial that is part of a master bioplate event.

newEventType() - Method in class net.sf.basedb.core.PlateType

Create a new event type for this plate type.

newExtract(Float) - Method in class net.sf.basedb.core.Sample

Create a new Extract from this sample.

newExtract(Float, BioPlateEventParticipant) - Method in class net.sf.basedb.core.Sample

Create a new Extract from this sample as part of a master bioplate event.

newExtraValue(Type, ExtraValue.CoordinateType) - Method in class net.sf.basedb.core.DataCube

Create a new extra vlaue in this data cube.

newFeature(ArrayDesignBlock, ReporterData) - Method in class net.sf.basedb.core.FeatureBatcher

Create a new feature.

newFeature(ArrayDesignBlock, Well) - Method in class net.sf.basedb.core.FeatureBatcher

Create a new feature.

newFilter() - Method in class net.sf.basedb.core.DataCube

Create a new filter in this datacube.

newHelp(String) - Method in class net.sf.basedb.core.Client

Create a new help text for this client.

newInstance() - Method in class net.sf.basedb.core.PluginDefinition

Get an unitialized instance of the plugin.

newInstance() - Static method in class net.sf.basedb.util.MD5

newInstance(Class<I>) - Static method in class net.sf.basedb.util.ClassUtil

Utility method for creating a new instance from a class with a default no-argument constructor.

newInstance(Class<P>) - Method in class net.sf.basedb.core.PluginDefinition

Get an unitialized instance of the plugin implementation.

newInstance(Class<P>, SessionControl, PluginConfiguration, Job) - Method in class net.sf.basedb.core.PluginDefinition

Get an initialized instance of the plugin implementation.

newInstance(ClassLoader, String, Class<I>, Class<?>...) - Static method in class net.sf.basedb.util.ClassUtil

Utility method for creating a new instance from a class (given by name) with a default no-argument constructor.

newInstance(String) - Static method in class net.sf.basedb.util.JarClassLoader

Get a new class loader for the specified jar file.

newInstance(String, String, ClassLoader, boolean) - Method in class net.sf.basedb.core.PluginDefinition

Create a new object instance of the given class.

newInternalFile - Variable in class net.sf.basedb.core.File

The path to a newly uploaded file.

newItem - Variable in class net.sf.basedb.clients.web.taglib.Select

If the link is from a new item or an old item.

newItem(Class<I>, Object...) - Method in class net.sf.basedb.core.DbControl

Create a new item.

newJep(String, JepFunction...) - Static method in class net.sf.basedb.util.jep.Jep

Create a new JEP expression.

newJob(Experiment) - Method in class net.sf.basedb.core.PluginConfiguration

Create a new Job for this plugin configuration.

newLayer() - Method in class net.sf.basedb.core.DataCube

Create a new layer in this datacube.

NEWLINE - Static variable in class net.sf.basedb.clients.web.plugins.XMLTemplate

NEWLINE - Static variable in class net.sf.basedb.clients.web.util.HTML

newMapperIsNeeded - Static variable in class net.sf.basedb.clients.web.extensions.skin.ImageRemapperUtil

newParameterValueData() - Method in class net.sf.basedb.core.BooleanParameterType

Create a new BooleanParameterValueData object.

newParameterValueData() - Method in class net.sf.basedb.core.DateParameterType

Create a new DateParameterValueData object.

newParameterValueData() - Method in class net.sf.basedb.core.DoubleParameterType

Create a new DoubleParameterValueData object.

newParameterValueData() - Method in class net.sf.basedb.core.FileParameterType

Create a new ItemParameterValueData object.

newParameterValueData() - Method in class net.sf.basedb.core.FloatParameterType

Create a new FloatParameterValueData object.

newParameterValueData() - Method in class net.sf.basedb.core.IntegerParameterType

Create a new IntegerParameterValueData object.

newParameterValueData() - Method in class net.sf.basedb.core.ItemParameterType

Create a new ItemParameterValueData object.

newParameterValueData() - Method in class net.sf.basedb.core.LongParameterType

Create a new LongParameterValueData object.

newParameterValueData() - Method in class net.sf.basedb.core.ParameterType

Create a new ParameterValueData subclass which is used to store values of this value type in the database.

newParameterValueData() - Method in class net.sf.basedb.core.PasswordParameterType

Create a new StringParameterValueData object.

newParameterValueData() - Method in class net.sf.basedb.core.PathParameterType

Create a new TextParameterValueData object.

newParameterValueData() - Method in class net.sf.basedb.core.StringParameterType

Create a new TextParameterValueData object.

newParameterValueData() - Method in class net.sf.basedb.core.TimestampParameterType

Create a new TimestampParameterValueData object.

newParameterValueData() - Method in enum class net.sf.basedb.core.Type

Create a new ParameterValueData subclass which is used to store values of this value type in the database.

newParameterVersion - Variable in class net.sf.basedb.core.PluginConfiguration

newPinger(SessionControl) - Static method in class net.sf.basedb.core.Application

Create a new Pinger object that is used to keep a session control alive.

newPlate() - Method in class net.sf.basedb.core.PlateType

Create a new plate of this plate type.

newPlateType() - Method in class net.sf.basedb.core.PlateGeometry

Create a new PlateType of this geometry.

newPluginConfiguration() - Method in class net.sf.basedb.core.PluginDefinition

Create a new PluginConfiguration for this plugin.

newPluginSessionControl(SessionControl, PluginDefinition, Job) - Static method in class net.sf.basedb.core.Application

Create a new session control for executing plugins.

newProduct(String, String, boolean) - Method in class net.sf.basedb.core.Transformation

Create a new product bioassayset from this transformation.

newRawData() - Method in class net.sf.basedb.core.RawDataBatcher

Create a new raw data object.

newReporter(String) - Method in class net.sf.basedb.core.ReporterType

Create a new ReporterData object of this type.

newReporterCloneTable - Variable in class net.sf.basedb.core.Experiment

newRootBioAssay(Collection<RawBioAssay>) - Method in class net.sf.basedb.core.BioAssaySet

Create a new BioAssay with links to raw bioassays.

News - Class in net.sf.basedb.core

This class represents news items.

News(NewsData) - Constructor for class net.sf.basedb.core.News

NEWS - Enum constant in enum class net.sf.basedb.core.Item

The item is a News.

News.QueryRuntimeFilterImpl - Class in net.sf.basedb.core

newSample() - Method in class net.sf.basedb.core.BioSource

Create a new Sample from this biosource.

NewsData - Class in net.sf.basedb.core.data

This class holds information about news items.

NewsData() - Constructor for class net.sf.basedb.core.data.NewsData

newsDate - Variable in class net.sf.basedb.core.data.NewsData

newSession() - Static method in class net.sf.basedb.core.HibernateUtil

Create a new Hibernate session.

newSession(Connection) - Static method in class net.sf.basedb.core.HibernateUtil

newSession(Interceptor, Connection) - Static method in class net.sf.basedb.core.HibernateUtil

Create a new Hibernate session, optionally with an interceptor.

newSession(SessionBuilder<?>, DbControl) - Method in class net.sf.basedb.core.ServiceSessionControl

Create a new Hibernate session for the given session factory that is piggy-backed on the given DbControl transaction.

newSessionControl(String, String, String) - Static method in class net.sf.basedb.core.Application

Create a new SessionControl object.

newStatelessSession(Session) - Static method in class net.sf.basedb.core.HibernateUtil

newSubDirectory() - Method in class net.sf.basedb.core.Directory

Create a new subdirectory to this directory.

newSyncFilter(DbControl) - Method in class net.sf.basedb.core.ItemList

Creates a new sync filter for this list.

newThreads - Variable in class net.sf.basedb.util.timer.Scheduler

newTransaction(Session) - Static method in class net.sf.basedb.core.HibernateUtil

Create a new transaction for a session.

newTransformation(Job) - Method in class net.sf.basedb.core.BioAssaySet

Create a new transformation using this bioassayset as it's source bioassayset.

newTransformation(Job, Collection<RawBioAssay>) - Method in class net.sf.basedb.core.Experiment

Create a new root transformation for this experiment.

newValue - Variable in class net.sf.basedb.core.data.ChangeHistoryDetailData

newValue - Variable in class net.sf.basedb.core.log.ManualLogEntry

newValues - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo

newVariant(String) - Method in class net.sf.basedb.core.Platform

Create a new PlatformVariant of this platform.

next - Variable in class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator

next - Variable in class net.sf.basedb.core.FastAnnotationLoader.FastIterator

next - Variable in class net.sf.basedb.util.Tree.EntryIterator

The next element to return.

next() - Method in class net.sf.basedb.clients.web.fileupload.FileUpload

Read from the input stream until a file section is found or the end is encountered.

next() - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator

next() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef.NullIterator

next() - Method in class net.sf.basedb.core.DataResultIterator

next() - Method in class net.sf.basedb.core.DynamicResultIterator

Get the results in the next row.

next() - Method in class net.sf.basedb.core.FastAnnotationLoader.FastIterator

next() - Method in class net.sf.basedb.core.ItemResultIterator

next() - Method in class net.sf.basedb.core.ItemResultList.ResultListIterator

next() - Method in class net.sf.basedb.core.ItemResultList.ResultListListIterator

next() - Method in class net.sf.basedb.core.ReporterScoreResultIterator

next() - Method in class net.sf.basedb.core.ScrollIterator

next() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter.FileIterator

next() - Method in class net.sf.basedb.util.ArrayIterator

next() - Method in class net.sf.basedb.util.extensions.ActionIterator

next() - Method in class net.sf.basedb.util.NestedIterator

next() - Method in class net.sf.basedb.util.query.MultiQueryIterator

next() - Method in class net.sf.basedb.util.Tree.ElementIterator

next() - Method in class net.sf.basedb.util.Tree.EntryIterator

nextBioAssay - Variable in class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter

nextBuffer - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream

nextCleanup - Variable in class net.sf.basedb.util.listable.TransformCache

nextCommand - Variable in class net.sf.basedb.core.PluginResponse

nextData - Variable in class net.sf.basedb.util.parser.FlatFileParser

The next available data line as parsed by the FlatFileParser.hasMoreData() method.

nextData() - Method in class net.sf.basedb.util.bfs.AnnotationParser

Get the next data line in the annotations file.

nextData() - Method in class net.sf.basedb.util.bfs.DataParser

Get the next data line in the file.

nextData() - Method in class net.sf.basedb.util.parser.FlatFileParser

Get the next available data.

nextElement - Variable in class net.sf.basedb.core.ScrollIterator

nextEnd - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream

nextEntry() - Method in class net.sf.basedb.util.bfs.MetadataParser

Get the next entry in the current section.

nextFileNum - Variable in class net.sf.basedb.util.bfs.SequenceFilenameGenerator

nextHop - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemMultiHopColumn

nextIndex - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil.WorkbookStream

nextIndex() - Method in class net.sf.basedb.core.ItemResultList.ResultListListIterator

nextIterator() - Method in class net.sf.basedb.core.FastAnnotationLoader.FastIterator

Create a new query that load annotations for items between startIndex and endIndex.

nextProgress - Variable in class net.sf.basedb.util.ProgressInputStream

nextProgressReport - Variable in class net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser

nextProgressReport - Variable in class net.sf.basedb.util.importer.spotdata.SecondPassSectionSpotsParser

nextProgressReport - Variable in class net.sf.basedb.util.importer.spotdata.SectionReporterListParser

nextQuery - Variable in class net.sf.basedb.util.query.MultiQueryIterator

nextReport - Variable in class net.sf.basedb.util.importer.spotdata.BfsImporter.ProgressEventHandler

nextSection - Variable in class net.sf.basedb.util.parser.FlatFileParser

The line that last matched the FlatFileParser.section.

nextSection() - Method in class net.sf.basedb.util.bfs.MetadataParser

Parse to the next section in the metadata file.

nextSection() - Method in class net.sf.basedb.util.parser.FlatFileParser

Get the next line that matches the section regular expression.

nextSheet() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.WorkbookStream

Switch to the next worksheet.

nextSpec - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemMultiHopColumn

nextStatusUpdateRequest - Variable in class net.sf.basedb.core.InternalJobQueue

Time when the next status update request for external jobs is scheduled.

nextStream() - Method in class net.sf.basedb.util.InputStreamCombiner

nextTick - Variable in class net.sf.basedb.core.Migration.ProgressInputStream

nextToken(String) - Method in class net.sf.basedb.util.jep.FunctionSafeJep.SafeFunctionTable

Get the next token in the parser.

nextValueType - Variable in class net.sf.basedb.util.parser.ColFunction

niceFormat(String) - Static method in class net.sf.basedb.clients.web.util.HTML

A convenience method for doing encodeTags(in, SAFE_TAGS), scanForLinks(in, "_blank") and formatLineBreaks(in) in a single operation.

niceFormat(String, int) - Static method in class net.sf.basedb.clients.web.util.HTML

A convenience method for doing encodeTags(in, SAFE_TAGS), scanForLinks(in, flags, "_blank") and formatLineBreaks(in) in a single operation.

niceFormat(String, int, String) - Static method in class net.sf.basedb.clients.web.util.HTML

A convenience method for doing encodeTags(in, SAFE_TAGS), scanForLinks(in, flags, link_target) and formatLineBreaks(in) in a single operation.

niceFormat(String, String) - Static method in class net.sf.basedb.clients.web.util.HTML

A convenience method for doing encodeTags(in, SAFE_TAGS), scanForLinks(in, target) and formatLineBreaks(in) in a single operation.

NiceFormatter - Class in net.sf.basedb.clients.web.formatter

Nicely format a string for output on a web page.

NiceFormatter() - Constructor for class net.sf.basedb.clients.web.formatter.NiceFormatter

Create a new formatter with default options: HTML.LINK_EMAIL + HTML.LINK_URL + HTML.SMART_IMAGES

NiceFormatter(int) - Constructor for class net.sf.basedb.clients.web.formatter.NiceFormatter

Create a new formatter with options.

NO - Enum constant in enum class net.sf.basedb.core.ItemContext.AddFilter

Do not any filter.

NO_AUTO_JOIN_PREFIXES - Static variable in class net.sf.basedb.core.ItemContext

NO_CANCELBUTTON - Static variable in class net.sf.basedb.clients.web.ModeInfo

NO_CHANGE - Enum constant in enum class net.sf.basedb.core.AnnotationBatcher.Change

The annotation was not changed.

NO_CHECK - Static variable in class net.sf.basedb.clients.web.ModeInfo

NO_CLOSEBUTTON - Static variable in class net.sf.basedb.clients.web.ModeInfo

NO_EDITLINK - Static variable in class net.sf.basedb.clients.web.ModeInfo

NO_FILTER - Static variable in class net.sf.basedb.clients.web.ModeInfo

NO_ICONS - Static variable in class net.sf.basedb.clients.web.ModeInfo

NO_NAVIGATOR - Static variable in class net.sf.basedb.clients.web.ModeInfo

NO_OKBUTTON - Static variable in class net.sf.basedb.clients.web.ModeInfo

NO_PERMISSION - Static variable in class net.sf.basedb.clients.web.ModeInfo

NO_PLUGIN - Static variable in class net.sf.basedb.core.PluginPermission

NO_PROPERTYLINK - Static variable in class net.sf.basedb.clients.web.ModeInfo

NO_RADIO - Static variable in class net.sf.basedb.clients.web.ModeInfo

NO_TOOLBAR - Static variable in class net.sf.basedb.clients.web.ModeInfo

noAutoCompression - Static variable in class net.sf.basedb.core.Application

If auto-compression has been enabled or not.

NoAutoUnlinkAnyToAny - Interface in net.sf.basedb.core.data

Tagging interface for items that are unlikely to be linked via an AnyToAny link.

node - Variable in class net.sf.basedb.core.data.JobData

node - Variable in class net.sf.basedb.core.Job.ProgressReporterImpl

node - Variable in class net.sf.basedb.util.overview.Failure

node - Variable in class net.sf.basedb.util.Tree.Entry

Node - Class in net.sf.basedb.util.overview

A node in an overview.

Node(String, String, BasicItem) - Constructor for class net.sf.basedb.util.overview.Node

Create an item-type root node.

Node(String, String, Node) - Constructor for class net.sf.basedb.util.overview.Node

Create a folder-type child node.

Node(String, String, Node, BasicItem) - Constructor for class net.sf.basedb.util.overview.Node

Create an item-type child node

Node(String, String, Node, BasicItem, ChildNodeDirection) - Constructor for class net.sf.basedb.util.overview.Node

Create an item-type child node

Node(String, String, Node, BasicItem, Node.Type, ChildNodeDirection) - Constructor for class net.sf.basedb.util.overview.Node

Node(String, String, Node, ChildNodeDirection) - Constructor for class net.sf.basedb.util.overview.Node

Create a folder-type child node.

Node(Node, Node) - Constructor for class net.sf.basedb.util.overview.Node

Make a copy of a node

Node.Type - Enum Class in net.sf.basedb.util.overview

The type of node.

NodeAttribute<T> - Class in net.sf.basedb.util.overview

Defines per-node attributes that can be used to store extra information together with a node that doesn't fit the regular properties.

NodeAttribute() - Constructor for class net.sf.basedb.util.overview.NodeAttribute

nodeCache - Variable in class net.sf.basedb.util.overview.GenericOverview

NodeCache<K> - Class in net.sf.basedb.util.overview.cache

A cache implementation for nodes.

NodeCache() - Constructor for class net.sf.basedb.util.overview.cache.NodeCache

NodeFactory<I extends BasicItem> - Class in net.sf.basedb.util.overview.node

A node factory is responsible for creating item-type nodes.

NodeFactory(DbControl, OverviewContext, NodeValidator<? super I>, NodeNameGenerator<? super I>) - Constructor for class net.sf.basedb.util.overview.node.NodeFactory

Create a node factory.

nodeId - Variable in class net.sf.basedb.util.overview.Node

NodeLoader<I> - Interface in net.sf.basedb.util.overview.loader

A node loader is an object that knows how to create a node for some specific item and how to load forward and reverse nodes for related items.

nodeLoaderFactory - Variable in class net.sf.basedb.util.overview.GenericOverview

NodeLoaderFactory<L,K> - Interface in net.sf.basedb.util.overview.loader

A node loader factory is a class that know how to create NodeLoader:s for a given key domain.

NodeNameGenerator<I> - Interface in net.sf.basedb.util.overview.node

A name generator is an object that can create the name and title for a node when given the item that should be attached to the node.

nodeToExpression(Node) - Static method in class net.sf.basedb.util.jep.Jep

Convert a node with it's children to an expression.

nodeToInt(Node) - Static method in class net.sf.basedb.util.jep.Jep

Convert a node to an integer value.

nodeToRestriction(Node) - Static method in class net.sf.basedb.util.jep.Jep

Convert a node with it's children to a restriction.

nodeToString(Node) - Static method in class net.sf.basedb.util.jep.Jep

Convert a node to a string value.

nodeType - Variable in class net.sf.basedb.util.overview.filter.NodeTypeFilter

NodeTypeFilter - Class in net.sf.basedb.util.overview.filter

A filter implementation that matches the node type.

NodeTypeFilter(Node.Type) - Constructor for class net.sf.basedb.util.overview.filter.NodeTypeFilter

Create a filter that finds nodes of the given node type.

NodeValidator<I> - Interface in net.sf.basedb.util.overview.validator

A node validator is responsible for checking the "validity" of a node.

NodeValidatorAction<I> - Interface in net.sf.basedb.util.overview.extensions

The same as a NodeValidator.

nodeValidatorFactory - Variable in class net.sf.basedb.util.overview.GenericOverview

NodeValidatorFactory<L,K> - Interface in net.sf.basedb.util.overview.validator

A node validator factory is a class that know how to create NodeValidator:s for a given key domain.

noDuplicates - Variable in class net.sf.basedb.util.annotations.InheritSpecification

NONDEFAULT_ARRAYDESIGN - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if an item uses a different array design than specified by the project default.

NONDEFAULT_HARDWARE - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if an item uses a different hardware than specified by the project default.

NONDEFAULT_PLATFORM - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if an item uses a different platform / variant than specified by the project default.

NONDEFAULT_PROTOCOL - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if an item uses a different protocol than specified by the project default.

NONDEFAULT_RAWDATATYPE - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if an item uses a different raw data type than specified by the project default.

NONDEFAULT_SOFTWARE - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if an item uses a different software than specified by the project default.

NONE - Enum constant in enum class net.sf.basedb.core.FeatureIdentificationMethod

None, because the array design is a file-only platform.

NONE - Enum constant in enum class net.sf.basedb.core.Formula.AverageMethod

NONE - Enum constant in enum class net.sf.basedb.core.IntensityTransform

No transformation has been applied to the spot intensities.

NONE - Enum constant in enum class net.sf.basedb.core.SyncFilter.SourceItemTransform

No transformation of source items is done.

NONE - Enum constant in enum class net.sf.basedb.util.overview.node.ChildNodeDirection

Represents an end-point node.

NoneOfFilter<T> - Class in net.sf.basedb.util.filter

A filter implementation that accpets an object only if at none of the parent filters accepts it.

NoneOfFilter(Collection<? extends Filter<? super T>>) - Constructor for class net.sf.basedb.util.filter.NoneOfFilter

Create a new filter.

NONMATCHING_SPOTCOUNT - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if the number of raw data spots are the same as the number of features (given a certain threshold).

NONMATHCING_ARRAYDESIGN - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if the array design for a raw bioassay matches the array design of the associated physical bioassay.

NonRestartable - Interface in net.sf.basedb.core.plugin

This is a tagging interface that should be implemented by the plug-ins that don't support restart and reconfiguration of a job after an interrupted execution.

NONUNIQUE_NAME_FOR_TYPE - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if two items of the same type has the same name.

NONUNIQUE_NAME_GLOBAL - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if two items of different type has the same name.

NONUNIQUE_TAG - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if a physical bioassay has more than one tagged extract with the same tag and position.

NoopPropertyPath(Class<C>, Type) - Constructor for class net.sf.basedb.core.Metadata.NoopPropertyPath

noPaging - Variable in class net.sf.basedb.core.ItemContext

noRawMapping - Variable in class net.sf.basedb.core.MappingBatcher

If the data cube has already received it's data and no raw data can be linked.

normalize(List<LowessNormalization.SpotData>, MACalculator) - Method in class net.sf.basedb.plugins.LowessNormalization.CallableWorker

Normalize the spot data.

normalize(DbControl, BioAssaySet, Job, float, float, float, int, ProgressReporter) - Method in class net.sf.basedb.plugins.MedianRatioNormalization

Normalise the source bioassay set using MEDIAN-RATIO normalization.

normalize(DbControl, BioAssaySet, Job, float, float, int, int, ProgressReporter) - Method in class net.sf.basedb.plugins.LowessNormalization

Normalise the source bioassay set using LOWESS normalization.

normalize(DbControl, BioAssaySet, Job, float, float, int, int, ReporterList, ProgressReporter) - Method in class net.sf.basedb.plugins.LowessNormalization

Normalise the source bioassay set using LOWESS normalization.

normalize1ch(DbControl, BioAssaySet, Job, float, float, float, ProgressReporter) - Method in class net.sf.basedb.plugins.MedianRatioNormalization

Normalise the source bioassay set using MEDIAN-RATIO normalization.

noSkin - Variable in class net.sf.basedb.clients.web.taglib.Page

Set to TRUE to not use skin on the page.

not(Restriction) - Static method in class net.sf.basedb.core.query.Restrictions

Negate a restriction: new restriction = NOT r

NOT - Enum constant in enum class net.sf.basedb.core.Operator

NOT_ANNOTATED - Enum constant in enum class net.sf.basedb.core.Include

Include items that have no annotations.

NOT_COMPACT - Static variable in class net.sf.basedb.clients.web.ModeInfo

NOT_REMOVED - Enum constant in enum class net.sf.basedb.core.Include

Include items flagged as not removed.

NOT_SELECTION_MODE - Static variable in class net.sf.basedb.clients.web.ModeInfo

noTabs - Variable in class net.sf.basedb.clients.web.taglib.tab.TabControl

If the tabs should be displayed or not.

notAmongSelected() - Method in class net.sf.basedb.core.AnnotationRestriction

If the main restriction should match items that had annotations among the selected annotation sets, or not.

notAmongSelected() - Method in class net.sf.basedb.core.HasAnnotationRestriction

NotConverter - Class in net.sf.basedb.util.jep.convert

Convert Not function to a Query API Restriction.

NotConverter() - Constructor for class net.sf.basedb.util.jep.convert.NotConverter

NotEqualsConverter - Class in net.sf.basedb.util.jep.convert

Convert the '!

NotEqualsConverter() - Constructor for class net.sf.basedb.util.jep.convert.NotEqualsConverter

notFound - Variable in class net.sf.basedb.util.extensions.xml.PluginInfo

notifyThread - Variable in class net.sf.basedb.clients.web.util.SimpleSignalProgressReporter

notifyThread - Variable in class net.sf.basedb.core.signal.AbstractSignalReceiver

notIn - Variable in class net.sf.basedb.core.query.IdListRestriction

NOTIN - Enum constant in enum class net.sf.basedb.core.Operator

NotInReporterListFunction - Class in net.sf.basedb.util.jep

A JEP function class that adds a notInList(reporterListId) function to a JEP expression parser.

NotInReporterListFunction(DbControl) - Constructor for class net.sf.basedb.util.jep.NotInReporterListFunction

Create a new instance of this function.

NOTLIKE - Enum constant in enum class net.sf.basedb.core.Operator

notLike_in(Expression, Expression...) - Static method in class net.sf.basedb.core.query.Restrictions

Check if one expression doesn't matches any of the expressions in an array.

NOTLIKE_IN - Enum constant in enum class net.sf.basedb.core.Operator

NotLoggable - Annotation Interface in net.sf.basedb.core.data

Getter methods that are annotated with this annotation should not trigger a log entry even if their values have changed.

notLoggableProperties - Variable in class net.sf.basedb.core.log.EntityLogOptions

NotLoggedInException - Exception in net.sf.basedb.core

This exception is thrown if you try to perform a function that requires a user to be logged in without beeing logged in.

NotLoggedInException() - Constructor for exception net.sf.basedb.core.NotLoggedInException

Creates a new NotLoggedInException.

notNull - Variable in class net.sf.basedb.core.ParameterType

If the parameter can be null or not.

NotNullFilter<T> - Class in net.sf.basedb.util.filter

A filter implementation that rejects all null objects.

NotNullFilter(boolean) - Constructor for class net.sf.basedb.util.filter.NotNullFilter

Create a new filter.

NotRestriction - Class in net.sf.basedb.core.query

Negate a restriction: NOT r

NotRestriction(Restriction) - Constructor for class net.sf.basedb.core.query.NotRestriction

noUsePermissionToReferenceErrorParameter - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

noUsePermissionToTargetErrorParameter - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

noWritePermissionToItemErrorParameter - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

noWritePermissionToItemErrorParameter - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

NULL_ESCAPE - Variable in class net.sf.basedb.core.migrate.AbstractResultWriter

NULL_ESCAPE - Variable in class net.sf.basedb.core.migrate.postgres.PostgresResultWriterFactory

PostgreSQL uses "\N" for null values.

nullable - Variable in class net.sf.basedb.core.data.ReporterClonePropertyData

nullable - Variable in class net.sf.basedb.core.ExtendedProperty

nullable - Variable in class net.sf.basedb.core.VirtualColumn

If the column should be nullable or not.

NULLABLE - Static variable in class net.sf.basedb.core.ClonableProperty

NULLABLE - Static variable in class net.sf.basedb.core.VirtualColumn

Used in constructor to tell that the column should be nullable.

nullIfException - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter

nullIfException - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

nullIfException - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

nullIfException - Variable in class net.sf.basedb.util.parser.ColumnMapper

nullIfException - Variable in class net.sf.basedb.util.parser.CompoundMapper

nullIfException - Variable in class net.sf.basedb.util.parser.ConstantMapper

NullIfExceptionMapper - Class in net.sf.basedb.util.parser

A mapper that returns null if there is an exception when parsing the input data.

NullIfExceptionMapper(Mapper) - Constructor for class net.sf.basedb.util.parser.NullIfExceptionMapper

Create a new CropStringMapper.

nullIfMissingReporter - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter

nullifyClonedReferences - Variable in class net.sf.basedb.core.AnnotationBatcher

nullIsEmptyString - Variable in class net.sf.basedb.util.encode.TabCrLfEncoderDecoder

nullIsNull - Variable in class net.sf.basedb.util.parser.FlatFileParser.Data

nullIsNull - Variable in class net.sf.basedb.util.parser.FlatFileParser

If null should be returned for the string NULL (ignoring case) or not.

NullIterator() - Constructor for class net.sf.basedb.clients.web.taglib.table.ColumnDef.NullIterator

NullNodeLoader<I> - Class in net.sf.basedb.util.overview.loader

A node loader implementation that doesn't load any nodes.

NullNodeLoader() - Constructor for class net.sf.basedb.util.overview.loader.NullNodeLoader

NullNodeValidator<I> - Class in net.sf.basedb.util.overview.validator

A node validator implementation that accepts all nodes, except missing items and denied access items (depending on configuration).

NullNodeValidator() - Constructor for class net.sf.basedb.util.overview.validator.NullNodeValidator

Create a new validator with default settings.

NullNodeValidator(boolean, boolean) - Constructor for class net.sf.basedb.util.overview.validator.NullNodeValidator

Created a new validator that accepts denied and/or missing nodes.

nullSafeAnd(Collection<? extends Restriction>) - Static method in class net.sf.basedb.core.query.Restrictions

Combine one or more restrictions with AND: new restriction = r[0] AND r[1] AND ...

nullSafeAnd(Restriction...) - Static method in class net.sf.basedb.core.query.Restrictions

Combine one or more restrictions with AND ignoring null elements.

nullSafeOr(Collection<? extends Restriction>) - Static method in class net.sf.basedb.core.query.Restrictions

Combine one or more restrictions with OR ignoring null elements.

nullSafeOr(Restriction...) - Static method in class net.sf.basedb.core.query.Restrictions

Combine one or more restrictions with OR ignoring null elements.

nullText - Variable in class net.sf.basedb.clients.web.taglib.PropertyValue

What to show if the value is null.

nullValue - Variable in class net.sf.basedb.clients.web.plugins.BioMaterialEventSourceFormatter

nullValue - Variable in class net.sf.basedb.core.log.ChangeTypeFormatter

nullValue - Variable in class net.sf.basedb.util.export.spotdata.ExportableFieldFormatter

nullValue - Variable in class net.sf.basedb.util.export.TableWriter

nullValue - Variable in class net.sf.basedb.util.formatter.EnumFormatter

nullValue - Variable in class net.sf.basedb.util.formatter.FilePathFormatter

nullValue - Variable in class net.sf.basedb.util.formatter.IdentifiableFormatter

nullValue - Variable in class net.sf.basedb.util.formatter.ItemTypeFormatter

nullValue - Variable in class net.sf.basedb.util.formatter.NameableFormatter

nullValue - Variable in class net.sf.basedb.util.formatter.ValueTypeFormatter

numAcceptedWithNullReporterOnFeature - Variable in class net.sf.basedb.core.RawDataBatcher

The number of accepted inserts were the feature had a NULL reporter

numAddedToList - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

numAnnotations - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations

numAnnotations - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

numArrays - Variable in class net.sf.basedb.core.data.ArrayDesignData

numArraysColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter

numArraysMapper - Variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter

NUMBER_FORMAT_ERROR - Static variable in class net.sf.basedb.plugins.util.Parameters

The name of the parameter created by Parameters.numberFormatError(String, String, String, String...).

NUMBER_OUT_OF_RANGE_ERROR - Static variable in class net.sf.basedb.plugins.util.Parameters

The name of the parameter created by Parameters.numberOutOfRangeError(String, String, String, String...).

numberFormat - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

numberFormat - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

numberFormat - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil

numberFormat - Variable in class net.sf.basedb.util.parser.ColFunction

numberFormat - Variable in class net.sf.basedb.util.parser.FlatFileParser

The default number formatter to use for creating mappers.

numberFormat - Variable in class net.sf.basedb.util.parser.JepMapper

numberFormat(int) - Static method in class net.sf.basedb.util.excel.ExcelValue

Creates a format string for formatting numbers with the given number of decimals (between 0 and 15).

numberFormatError(String, String, String, String...) - Static method in class net.sf.basedb.plugins.util.Parameters

Create the parameter for handling invalid numbers.

numberFormatErrorParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter

numberFormatErrorParameter - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

NumberFormatFormatter - Class in net.sf.basedb.util.formatter

Formatter implementation for numeric values that simply wrap a NumberFormat instance.

NumberFormatFormatter(NumberFormat) - Constructor for class net.sf.basedb.util.formatter.NumberFormatFormatter

Create a new number formatter.

numberFormatter - Variable in class net.sf.basedb.clients.web.formatter.ColorFormatter

NumberFormatter - Class in net.sf.basedb.util.formatter

Formats a number for output on a web page.

NumberFormatter(int, boolean) - Constructor for class net.sf.basedb.util.formatter.NumberFormatter

Create a new number formatter.

NumberFormatUtil - Class in net.sf.basedb.util

Utility class for working with NumberFormat object.

NumberFormatUtil() - Constructor for class net.sf.basedb.util.NumberFormatUtil

numberOfRows - Variable in class net.sf.basedb.core.dbengine.TableInfo

numberOutOfRangeError(String, String, String, String...) - Static method in class net.sf.basedb.plugins.util.Parameters

Create the parameter for handling numeric values that are outside the allowed range.

numberOutOfRangeErrorParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter

numberOutOfRangeErrorParameter - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

NumberOutOfRangeException - Exception in net.sf.basedb.core

This exception is thrown when an item's field or a parameter that only accepts numeric values within a certain range are passed a value outside that range.

NumberOutOfRangeException() - Constructor for exception net.sf.basedb.core.NumberOutOfRangeException

Create a new NumberOutOfRangeException object.

NumberOutOfRangeException(String) - Constructor for exception net.sf.basedb.core.NumberOutOfRangeException

NumberOutOfRangeException(String, double, double, boolean) - Constructor for exception net.sf.basedb.core.NumberOutOfRangeException

Create a new NumberOutOfRangeException object when the parameter is less than a minimum or greater than a maximum value.

NumberOutOfRangeException(String, double, double, double) - Constructor for exception net.sf.basedb.core.NumberOutOfRangeException

Create a new NumberOutOfRangeException object when the parameter is outside both a minimum and a maximum allowed value.

NumberOutOfRangeException(String, long, long, boolean) - Constructor for exception net.sf.basedb.core.NumberOutOfRangeException

Create a new NumberOutOfRangeException object when the parameter is less than a minimum or greater than a maximum value.

NumberOutOfRangeException(String, long, long, long) - Constructor for exception net.sf.basedb.core.NumberOutOfRangeException

Create a new NumberOutOfRangeException object when the parameter is outside both a minimum and a maximum allowed value.

numBlocks - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter

numBlocks - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

numChannels - Variable in class net.sf.basedb.core.SpotBatcher

The number of channels used in the raw data type of the experiment where the bioassayset belongs.

numChildren() - Method in class net.sf.basedb.util.overview.Node

Get the number of child nodes in this node.

numColumns - Variable in class net.sf.basedb.clients.web.taglib.table.HeaderRow

numColumns - Variable in class net.sf.basedb.core.data.DataCubeData

numColumns - Variable in class net.sf.basedb.util.bfs.AnnotationParser

numColumns - Variable in class net.sf.basedb.util.bfs.DataParser

numColumns - Variable in class net.sf.basedb.util.bfs.MatrixModel

numCreated - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

numCreated - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

numDataColumnsType - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter

numDecimals - Variable in class net.sf.basedb.util.formatter.NumberFormatter

numDeleted - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

numDeleted - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsManager

numDeleted - Variable in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor

numElements - Variable in class net.sf.basedb.clients.web.taglib.path.Path

Keeps track of the number of path elements so separators can be added.

numEntries - Variable in class net.sf.basedb.util.extensions.logging.ExtensionsLog

numericToAlpha(int) - Static method in class net.sf.basedb.util.Coordinate

Convert a numeric coordinate to an alphanumeric coordinate.

NumericValue(Number, String) - Constructor for class net.sf.basedb.util.excel.ExcelValue.NumericValue

numError - Variable in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor

numError - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations

numError - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

numError - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

numError - Variable in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor

numError - Variable in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor

numError - Variable in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor

numError - Variable in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor

numError - Variable in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor

numError - Variable in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor

numErrorFiles - Variable in class net.sf.basedb.util.extensions.manager.ProcessResults

numErrors - Variable in class net.sf.basedb.util.extensions.logging.ExtensionsLog

numErrors - Variable in class net.sf.basedb.util.overview.Node

numExisted - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

numExists - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

numExported - Variable in class net.sf.basedb.plugins.GalExporter

numExported - Variable in class net.sf.basedb.plugins.HelpExporter

numExported - Variable in class net.sf.basedb.plugins.PluginConfigurationExporter

numExtraValues - Variable in class net.sf.basedb.core.data.DataCubeData

numFeatures - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter

numFeatures - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

numFileReporters - Variable in class net.sf.basedb.core.data.BioAssaySetData

numFiles - Variable in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor

numFiles - Variable in class net.sf.basedb.clients.web.extensions.UninstalledFileProcessor

numFiles - Variable in class net.sf.basedb.plugins.PackedFileExporter

numFiles - Variable in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor

numFiles - Variable in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor

numFiles - Variable in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor

numFiles - Variable in class net.sf.basedb.util.extensions.manager.processor.IgnoreFileProcessor

numFiles - Variable in class net.sf.basedb.util.extensions.manager.processor.MarkAsProcessedProcessor

numFiles - Variable in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor

numFiles - Variable in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor

numFiles - Variable in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor

numFiles - Variable in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor

numFileSpots - Variable in class net.sf.basedb.core.data.BioAssayData

numFileSpots - Variable in class net.sf.basedb.core.data.BioAssaySetData

numFileValues - Variable in class net.sf.basedb.core.data.ExtraValueData

numFilteredColumns - Variable in class net.sf.basedb.clients.web.taglib.table.Table

numFilterRows - Variable in class net.sf.basedb.clients.web.taglib.table.Table

Number of filter rows in the table.

numFilterRows - Variable in class net.sf.basedb.core.ItemContext

numFilterRows - Variable in class net.sf.basedb.core.SyncFilter

numFilters - Variable in class net.sf.basedb.core.data.DataCubeData

numHeaderColumns - Variable in class net.sf.basedb.clients.web.taglib.table.Table

numHeaderColumns() - Method in class net.sf.basedb.clients.web.taglib.table.Table

numIgnored - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsManager

numImported - Variable in class net.sf.basedb.plugins.HelpImporter

numInserted - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter

numInserted - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

numItemNotFound - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

numItems - Variable in class net.sf.basedb.core.AnnotationBatcher

numItems - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

numLayers - Variable in class net.sf.basedb.core.data.DataCubeData

numLines - Variable in class net.sf.basedb.core.Migration.ProgressInputStream

numModified - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsManager

numMultiLines - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

numNew - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsManager

numNewChildren() - Method in class net.sf.basedb.util.overview.Node

Get the number of new children added to this node since the last call to Node.getNewChildren().

numNotFound - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

numNotFound - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

numParameters - Variable in class net.sf.basedb.util.jep.ChannelFunction

numParameters - Variable in class net.sf.basedb.util.jep.ExtraValueFunction

numParameters - Variable in class net.sf.basedb.util.jep.InReporterListFunction

numParameters - Variable in class net.sf.basedb.util.jep.MeanFunction

numParameters - Variable in class net.sf.basedb.util.jep.NotInReporterListFunction

numParameters - Variable in class net.sf.basedb.util.jep.RawChannelFunction

numParameters - Variable in class net.sf.basedb.util.jep.RawFunction

numParameters - Variable in class net.sf.basedb.util.jep.ReporterFunction

numParameters - Variable in class net.sf.basedb.util.jep.ScoreFunction

numParameters - Variable in class net.sf.basedb.util.jep.SimpleJepFunction

numParameters - Variable in class net.sf.basedb.util.parser.DefaultItemFunction

numPlates - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter

numPositions - Variable in class net.sf.basedb.core.data.DataCubeData

numRawBioAssays - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter

numRead - Variable in class net.sf.basedb.util.InputStreamSplitter

numRead - Variable in class net.sf.basedb.util.InputStreamTracker

The number of bytes that has been read from the underlying input stream so far.

numReadAtMark - Variable in class net.sf.basedb.util.InputStreamTracker

The number of bytes that had been read when InputStreamTracker.mark(int) was called.

numRegistered - Variable in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor

numRemoved - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations

numRemoved - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

numRemoved - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

numReplaced - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations

numReplaced - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

numReporters - Variable in class net.sf.basedb.core.data.BioAssaySetData

numReportersNotFound - Variable in class net.sf.basedb.core.RawDataBatcher

The number of reporters that was not found.

numReturned - Variable in class net.sf.basedb.util.query.MultiQueryIterator

numRows(long) - Method in class net.sf.basedb.core.Migration

numRowsFormat - Variable in class net.sf.basedb.core.Migration

numSelected - Variable in class net.sf.basedb.plugins.PluginConfigurationExporter

numServlets - Variable in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor

numSet - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations

numSkipped - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

numSkippedMissingFeature - Variable in class net.sf.basedb.core.RawDataBatcher

The number of skipped inserts due to missing feature

numSpots - Variable in class net.sf.basedb.core.data.BioAssayData

numSpots - Variable in class net.sf.basedb.core.data.BioAssaySetData

numStatements - Variable in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget

numTabs - Variable in class net.sf.basedb.clients.web.taglib.tab.TabControl

The number of tabs.

numTotal - Variable in class net.sf.basedb.plugins.HelpImporter

numTotalExtracted - Variable in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor

numTotalPlugins - Variable in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor

numTotalPlugins - Variable in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor

numUnmodified - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsManager

numUnregistered - Variable in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor

numUnregistered - Variable in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor

numUpdated - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

numUpdated - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

numUpdated - Variable in class net.sf.basedb.plugins.HelpImporter

numUpdated - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

numUsed - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

numValues - Variable in class net.sf.basedb.core.data.ExtraValueData

numVisibleColumns() - Method in class net.sf.basedb.clients.web.taglib.table.Table

numWarnings - Variable in class net.sf.basedb.util.extensions.logging.ExtensionsLog

numWarnings - Variable in class net.sf.basedb.util.overview.Node

numWells - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter

O

object - Variable in class net.sf.basedb.util.filter.EqualsFilter

object - Variable in class net.sf.basedb.util.filter.IdentityFilter

objectCache - Variable in class net.sf.basedb.util.overview.GenericOverview

ObjectKey<O> - Interface in net.sf.basedb.util.extensions.manager

Instances of object keys should be something that uniquely identifies an object that has been defined by an extension.

objectMetadata - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile

objects - Variable in class net.sf.basedb.core.ItemContext

objects - Variable in class net.sf.basedb.util.ClassLocal

OFF - Enum constant in enum class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory.Level

OFFLINE - Enum constant in enum class net.sf.basedb.core.Location

The item is offline and doesn't use any quota.

offset - Variable in class net.sf.basedb.core.Job.ProgressReporterImpl

offset - Variable in class net.sf.basedb.util.extensions.ActionIterator

offset - Variable in class net.sf.basedb.util.units.LinearUnitConverter

offsetMid - Variable in class net.sf.basedb.util.ColorGenerator

The RGB components of the midpoint color. [0] = red; [1] = green; [2] = blue

offsetMin - Variable in class net.sf.basedb.util.ColorGenerator

The RGB components of the min color. [0] = red; [1] = green; [2] = blue

olderThan(long) - Method in class net.sf.basedb.util.StaticCache

Creates a file filter that matches all files that are older than the specified age.

OlderThanFileFilter - Class in net.sf.basedb.util

An implementation of the FileFilter interface that filter files based on their age.

OlderThanFileFilter(long, boolean) - Constructor for class net.sf.basedb.util.OlderThanFileFilter

Create a new file filter that matches files that are older than the specified age.

oldFileResults - Variable in class net.sf.basedb.util.extensions.manager.ProcessResults

oldPropertyValues - Variable in class net.sf.basedb.core.log.db.AnnotationSetLogger

oldPropertyValues - Variable in class net.sf.basedb.core.log.db.BioMaterialEventLogger

oldPropertyValues - Variable in class net.sf.basedb.core.log.db.DbLogManagerFactory

oldPropertyValues - Variable in class net.sf.basedb.core.log.db.DefaultEntityLogger

oldPropertyValues - Variable in class net.sf.basedb.core.log.db.ManualEntryLogger

oldReporterCloneTable - Variable in class net.sf.basedb.core.Experiment

oldValue - Variable in class net.sf.basedb.clients.web.plugins.ChangeHistoryDetailLoader

oldValue - Variable in class net.sf.basedb.core.data.ChangeHistoryDetailData

oldValue - Variable in class net.sf.basedb.core.log.ManualLogEntry

oldValues - Variable in class net.sf.basedb.core.data.ParameterValueData

on - Variable in class net.sf.basedb.core.query.HqlInnerJoin

on - Variable in class net.sf.basedb.core.query.HqlLeftJoin

on - Variable in class net.sf.basedb.core.query.HqlRightJoin

ON_COMMIT - Static variable in class net.sf.basedb.clients.web.extensions.edit.OnSaveRenderer

Renderer that calls the OnSaveAction.onCommit() method.

ON_SAVE - Static variable in class net.sf.basedb.clients.web.extensions.edit.OnSaveRenderer

Renderer that calls the OnSaveAction.onSave() method.

onAdd(BioWellData, MeasuredBioMaterialData) - Method in enum class net.sf.basedb.core.BioWell.LockMode

Called when biomaterial is added to a well.

onAfterCommit() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper.CloseMyDbControl

onAfterCommit() - Method in class net.sf.basedb.core.AnnotationType.RemoveInheritedAnnotationsAction

onAfterCommit() - Method in class net.sf.basedb.core.DerivedBioAssay.FixDerivedBioAssayParentsRecursivelyAction

onAfterCommit() - Method in class net.sf.basedb.core.DropDynamicTableAction

onAfterCommit() - Method in class net.sf.basedb.core.ItemList.DelayedAdditionManager

onAfterCommit() - Method in class net.sf.basedb.core.Job.JobSignalTransporter

onAfterCommit() - Method in class net.sf.basedb.core.MeasuredBioMaterial.RemainingQuantityAction

onAfterCommit() - Method in class net.sf.basedb.core.ProjectSpecificAnnotationsManager

onAfterCommit() - Method in class net.sf.basedb.core.ServiceSessionControl.FlushSessionAction

onAfterCommit() - Method in interface net.sf.basedb.core.TransactionalAction

Called after a successful commit.

onAfterCommit(Transactional.Action) - Method in class net.sf.basedb.core.BasicItem

This method is called on each Transactional object after a successful commit to the database.

onAfterCommit(Transactional.Action) - Method in class net.sf.basedb.core.Experiment

Remove old reporter clone table after a successful commit.

onAfterCommit(Transactional.Action) - Method in class net.sf.basedb.core.File

onAfterCommit(Transactional.Action) - Method in class net.sf.basedb.core.Job

If the Signal.ABORT signal is waiting to be sent send it.

onAfterCommit(Transactional.Action) - Method in class net.sf.basedb.core.Message

Send the message as an email if requested by the user.

onAfterCommit(Transactional.Action) - Method in class net.sf.basedb.core.Platform

Register file-only platforms as raw data type after insert and unregister after delete.

onAfterCommit(Transactional.Action) - Method in class net.sf.basedb.core.PlatformVariant

Register file-only platforms as raw data type after insert and unregister after delete.

onAfterCommit(Transactional.Action) - Method in class net.sf.basedb.core.PluginConfiguration

Reset parameter version so that adding new parameters will increase the version the next time.

onAfterCommit(Transactional.Action) - Method in class net.sf.basedb.core.VirtualDb

Remove all dynamic tables if action == Action.DELETE

onAfterInsert() - Method in class net.sf.basedb.core.Annotation

onAfterInsert() - Method in class net.sf.basedb.core.BasicItem

This method is called on all items directly after Hibernate has inserted it into the database.

onAfterInsert() - Method in class net.sf.basedb.core.BioPlateEventType

onAfterInsert() - Method in class net.sf.basedb.core.PluginDefinition

onBeforeClose() - Method in class net.sf.basedb.core.AbstractBatcher

Let a subclass cleanup itself before the connection to the database is closed.

onBeforeClose() - Method in class net.sf.basedb.core.AnnotationBatcher

onBeforeClose() - Method in class net.sf.basedb.core.BasicBatcher

Close all open SQL statements.

onBeforeClose() - Method in class net.sf.basedb.core.FeatureBatcher

Set the hasFeature flag on the array design if features has been added.

onBeforeClose() - Method in class net.sf.basedb.core.FilterBatcher

Close open SQL statements.

onBeforeClose() - Method in class net.sf.basedb.core.MappingBatcher

Update bytes on data cube and close open SQL statements.

onBeforeClose() - Method in class net.sf.basedb.core.PositionBatcher

Update bytes and max position on the datacube and close open SQL statements.

onBeforeClose() - Method in class net.sf.basedb.core.PositionExtraValueBatcher

Update disk usage and close open SQL statements

onBeforeClose() - Method in class net.sf.basedb.core.RawDataBatcher

Update the spot count and disk usage on the raw bioassay.

onBeforeClose() - Method in class net.sf.basedb.core.ReporterCloneBatcher

Update disk usage and close open SQL statements.

onBeforeClose() - Method in class net.sf.basedb.core.SpotBatcher

Update disk usage and close open SQL statements

onBeforeClose() - Method in class net.sf.basedb.core.SpotExtraValueBatcher

Update disk usage and close open SQL statements

onBeforeCommit() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper.CloseMyDbControl

onBeforeCommit() - Method in class net.sf.basedb.core.AnnotationType.RemoveInheritedAnnotationsAction

onBeforeCommit() - Method in class net.sf.basedb.core.DerivedBioAssay.FixDerivedBioAssayParentsRecursivelyAction

onBeforeCommit() - Method in class net.sf.basedb.core.DropDynamicTableAction

onBeforeCommit() - Method in class net.sf.basedb.core.ItemList.DelayedAdditionManager

onBeforeCommit() - Method in class net.sf.basedb.core.MeasuredBioMaterial.RemainingQuantityAction

onBeforeCommit() - Method in class net.sf.basedb.core.ProjectSpecificAnnotationsManager

onBeforeCommit() - Method in class net.sf.basedb.core.ServiceSessionControl.FlushSessionAction

onBeforeCommit() - Method in interface net.sf.basedb.core.TransactionalAction

This method is called before the commit is about to happen.

onBeforeCommit(D, Transactional.Action) - Method in class net.sf.basedb.core.BasicBatcher

Called after the object has been validated just before the SQL is added to the batch queue.

onBeforeCommit(ReporterData, Transactional.Action) - Method in class net.sf.basedb.core.ReporterBatcher

Set the last update date to today's date and change the last source of update.

onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.Annotation

Nullify links to this annotation from cloned annotations when this annotation is deleted (since the cloned annotation should not be deleted).

onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.AnnotationSet

Remove the cached snapshot if needed.

onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.AnyToAny

We may have to set the AnyToAny.getFromId() and/or AnyToAny.getToId() values if those items are also created in the same transaction.

onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.BasicItem

This method is called on each Transactional item and on all items if the action is Transactional.Action.CREATE or Transactional.Action.DELETE before a commit is issued to the database.

onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.BioAssay

onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.BioAssaySet

On creation, count the number of spots and reporters in the bioassays attached to this bioassayset.

onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.BioMaterialEvent

Return used guantity to biomaterials on delete action.

onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.BioPlate

onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.BioPlateEvent

onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.BioPlateEventParticipant

onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.DataCube

Delete data and update disk usage information on the experiment if action == Action.DELETE

onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.DataCubeExtraValue

Delete data and update disk usage information on the experiment if action == Action.DELETE

onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.DataCubeFilter

Delete data and update disk usage information on the experiment if action == Action.DELETE

onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.DataCubeLayer

Delete data and update disk usage information on the experiment if action == Action.DELETE

onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.DerivedBioAssay

Automatically try to assign an extract from parent items at creation time.

onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.Experiment

onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.File

onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.Group

Set group to null in disk usage where this group is referenced.

onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.Job

Set's the project id to the currently active project.

onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.MeasuredBioMaterial

Make sure the creation event is created at the same time this item is created and that source biomaterials get their used quantities back if this item is deleted.

onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.OwnedItem

Overrides the BasicItem.onBeforeCommit(Transactional.Action) method.

onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.PhysicalBioAssay

Make sure the creation event is created at the same time this item is created and that source biomaterials get their used quantities back if this item is deleted.

onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.Project

onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.RawBioAssay

Delete raw data if it exists.

onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.SharedItem

If a project is active, automatically share the new item according to the settings of that project, unless a project or item key has been explicitely set (including null).

onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.Transformation

Delete the product bioassaysets when deleting this transction.

onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.Unit

Set property filters that use this unit to null when the unit is deleted.

onClear(BioWellData, MeasuredBioMaterialData) - Method in enum class net.sf.basedb.core.BioWell.LockMode

Called when a well is cleared from an existing biomaterial.

onClick - Variable in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

onCommit() - Method in class net.sf.basedb.clients.web.extensions.edit.AbstractOnSaveAction

onCommit() - Method in class net.sf.basedb.clients.web.extensions.edit.DebugOnSaveActionFactory.DebugOnSaveAction

onCommit() - Method in interface net.sf.basedb.clients.web.extensions.edit.OnSaveAction

This event is fired after a successful commit.

onDelete(Object, Serializable, Object[], String[], Type[]) - Method in class net.sf.basedb.core.log.LoggingInterceptor

Adds a DELETE event to the log.

ONE_ZERO - Enum constant in enum class net.sf.basedb.util.formatter.BooleanFormatter.Type

Display 1/0.

OneOfFilter<T> - Class in net.sf.basedb.util.filter

A filter implementation that accpets an object if at least one parent filters accepts it.

OneOfFilter(Collection<? extends Filter<? super T>>) - Constructor for class net.sf.basedb.util.filter.OneOfFilter

Create a new filter.

onFlushDirty(Object, Serializable, Object[], Object[], String[], Type[]) - Method in class net.sf.basedb.core.log.LoggingInterceptor

Adds an UPDATE event to the log.

onRollback() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper.CloseMyDbControl

onRollback() - Method in class net.sf.basedb.core.AnnotationType.RemoveInheritedAnnotationsAction

onRollback() - Method in class net.sf.basedb.core.DerivedBioAssay.FixDerivedBioAssayParentsRecursivelyAction

onRollback() - Method in class net.sf.basedb.core.DropDynamicTableAction

onRollback() - Method in class net.sf.basedb.core.ItemList.DelayedAdditionManager

onRollback() - Method in class net.sf.basedb.core.MeasuredBioMaterial.RemainingQuantityAction

onRollback() - Method in class net.sf.basedb.core.ProjectSpecificAnnotationsManager

onRollback() - Method in class net.sf.basedb.core.ServiceSessionControl.FlushSessionAction

onRollback() - Method in interface net.sf.basedb.core.TransactionalAction

Called after an unsuccessful commit.

onRollback(Exception) - Method in class net.sf.basedb.clients.web.extensions.edit.AbstractOnSaveAction

onRollback(Exception) - Method in class net.sf.basedb.clients.web.extensions.edit.DebugOnSaveActionFactory.DebugOnSaveAction

onRollback(Exception) - Method in interface net.sf.basedb.clients.web.extensions.edit.OnSaveAction

This event is fired after an error that caused the save action to rollback.

onRollback(Exception) - Static method in class net.sf.basedb.clients.web.extensions.edit.OnSaveRenderer

Renderer that calls the OnSaveAction.onRollback(Exception) method.

onRollback(Transactional.Action) - Method in class net.sf.basedb.core.BasicItem

This method is called on each Transactional object after an unsuccessful commit to the database.

onRollback(Transactional.Action) - Method in class net.sf.basedb.core.Experiment

Remove new reporter clone table after a rollback.

onRollback(Transactional.Action) - Method in class net.sf.basedb.core.File

onSave() - Method in class net.sf.basedb.clients.web.extensions.edit.AbstractOnSaveAction

onSave() - Method in class net.sf.basedb.clients.web.extensions.edit.DebugOnSaveActionFactory.DebugOnSaveAction

onSave() - Method in interface net.sf.basedb.clients.web.extensions.edit.OnSaveAction

This event is fired first to let the action do something with the current item.

onSave(Object, Serializable, Object[], String[], Type[]) - Method in class net.sf.basedb.core.log.LoggingInterceptor

Adds a CREATE event to the log.

OnSaveAction - Interface in net.sf.basedb.clients.web.extensions.edit

Action that is called when an item is saved in gui.

OnSaveRenderer - Class in net.sf.basedb.clients.web.extensions.edit

Renderer implementations for OnSaveAction:s.

OnSaveRenderer() - Constructor for class net.sf.basedb.clients.web.extensions.edit.OnSaveRenderer

open - Variable in class net.sf.basedb.clients.web.taglib.menu.Menu

If submenus opens as soon as the mouse enters or a click is required.

open() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile

open() - Method in class net.sf.basedb.util.jobagent.JobAgentServerConnection

Start listening for incoming connections.

operator - Variable in class net.sf.basedb.core.AnnotationSimpleRestriction

operator - Variable in class net.sf.basedb.core.data.PropertyFilterData

operator - Variable in class net.sf.basedb.core.PropertyFilter

operator - Variable in class net.sf.basedb.core.query.SubqueryExpression

operator(String) - Method in class net.sf.basedb.util.formatter.PropertyFilterFormatter

Operator - Enum Class in net.sf.basedb.core

Operator(int, String, String, boolean, boolean, boolean) - Constructor for enum class net.sf.basedb.core.Operator

operators - Static variable in class net.sf.basedb.util.jep.Jep

optionalBooleanType - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

optionalBooleanType - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

optionalColumnMapping - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

optionalColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

optionalColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

optionalColumnMapping - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

optionalColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

optionalColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

optionalFilter - Variable in class net.sf.basedb.core.AbstractEntityQuery

Optional runtime filter.

optionalFilters - Static variable in class net.sf.basedb.core.QueryRuntimeFilterFactory

optionalNameType - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

A parameter type for name parameters which are optional.

optionalRegexpType - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter

optionalSaveAsType - Static variable in class net.sf.basedb.core.plugin.AbstractExporterPlugin

options - Variable in class net.sf.basedb.clients.jobagent.CmdLine

options - Variable in class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor

options - Variable in class net.sf.basedb.core.AnnotationRestriction

options - Variable in class net.sf.basedb.core.data.AnnotationTypeData

options - Static variable in class net.sf.basedb.core.log.EntityLogOptions

options - Variable in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter

options - Variable in class net.sf.basedb.plugins.executor.ParameterDefinition

options - Variable in class net.sf.basedb.util.overview.ValidationOptions

Other options.

Options() - Constructor for class net.sf.basedb.core.AnnotationRestriction.Options

Creates the default options.

Options() - Constructor for class net.sf.basedb.util.AnyToAnyLinkStatistics.Options

or(Restriction...) - Static method in class net.sf.basedb.core.query.Restrictions

Combine one or more restrictions with OR: new restriction = r[0] OR r[1] ...

OR - Enum constant in enum class net.sf.basedb.core.Operator

OrConverter - Class in net.sf.basedb.util.jep.convert

Convert the '||' operator to a Query API Restriction.

OrConverter() - Constructor for class net.sf.basedb.util.jep.convert.OrConverter

order(Order) - Method in class net.sf.basedb.core.AbstractQuery

order(Order) - Method in interface net.sf.basedb.core.query.Query

Add an ordering query element to the orderby list.

Order - Interface in net.sf.basedb.core.query

An ordering query element.

ORDERBY - Enum constant in enum class net.sf.basedb.core.query.QuerySection

orderPermanent(Order) - Method in class net.sf.basedb.core.AbstractQuery

orderPermanent(Order) - Method in interface net.sf.basedb.core.query.Query

Permanently add an ordering query element to the orderby list.

orders - Variable in class net.sf.basedb.core.AbstractQuery

List of orders added to the query.

Orders - Class in net.sf.basedb.core.query

A factory class to create order by expressions.

Orders() - Constructor for class net.sf.basedb.core.query.Orders

ordinal - Variable in class net.sf.basedb.core.data.PlateEventTypeData

organisation - Variable in class net.sf.basedb.core.authentication.ExtraUserInformation

organisation - Variable in class net.sf.basedb.core.data.UserData

original - Variable in class net.sf.basedb.core.hibernate.SchemaGenerator.SqlStatement

originalBioMaterial - Variable in class net.sf.basedb.core.data.BioWellData

originalPermissions - Variable in class net.sf.basedb.core.GroupPermissions

originalPermissions - Variable in class net.sf.basedb.core.ProjectPermissions

originalPermissions - Variable in class net.sf.basedb.core.UserPermissions

originalQuantity - Variable in class net.sf.basedb.core.data.MeasuredBioMaterialData

originalQuantityColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.SampleImporter

Column mapping parameter for the original quantity.

originalQuantityMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter

originalQuantityMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter

originalServletPath - Variable in class net.sf.basedb.clients.web.extensions.RequestWrapper

originX - Variable in class net.sf.basedb.core.data.ArrayDesignBlockData

originX - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock

originY - Variable in class net.sf.basedb.core.data.ArrayDesignBlockData

originY - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock

OrRestriction - Class in net.sf.basedb.core.query

Combine one or more restrictions with OR: r[0] OR r[1] OR ...

OrRestriction(Restriction...) - Constructor for class net.sf.basedb.core.query.OrRestriction

OTHER - Enum constant in enum class net.sf.basedb.core.BioMaterialEvent.Type

An event of this type affected a single biomaterial in some way.

OTHER - Enum constant in enum class net.sf.basedb.core.Job.Type

The job is executed by some other program.

OTHER - Enum constant in enum class net.sf.basedb.core.plugin.Plugin.MainType

OTHER - Static variable in class net.sf.basedb.core.Hardware

The id for the HardwareType object representing something else.

otherLogger - Variable in class net.sf.basedb.util.extensions.logging.ExtensionsLogger

OTHERS - Enum constant in enum class net.sf.basedb.core.Include

Include items owned by other users.

out - Variable in class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor.StreamRedirector

out - Variable in class net.sf.basedb.clients.web.plugins.XlsxTemplate

out - Variable in class net.sf.basedb.core.plugin.ExportOutputStream

out - Variable in class net.sf.basedb.util.export.spotdata.BaseFileExporter

out - Variable in class net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter

out - Variable in class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter

out - Variable in class net.sf.basedb.util.FileCopyRunnable

overridden - Static variable in class net.sf.basedb.core.Config

Properties that has been programmatically overridden.

override - Variable in class net.sf.basedb.clients.web.util.ProjectSpecificInfoFilter

overrideId - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo

overrideId - Variable in class net.sf.basedb.core.data.AnnotationData

overrideId - Variable in class net.sf.basedb.core.data.annotations.AnnotationLink

overrideId - Variable in class net.sf.basedb.core.FastAnnotationLoader.FastAnnotation

The ID of the default annotation this value is overriding.

overrideId - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot

overridesDefaultAnnotation() - Method in class net.sf.basedb.clients.web.util.ProjectSpecificInfoFilter

Check if the override flag is set.

OverviewContext - Interface in net.sf.basedb.util.overview

Interface that should be implemented by overview generating classes.

OverviewPlotAction - Interface in net.sf.basedb.clients.web.extensions.plot

Action for generating overview plots for a bioassay set.

OverviewPlotBean - Class in net.sf.basedb.clients.web.extensions.plot

A simple bean-like implementation of the OverviewPlotAction interface.

OverviewPlotBean() - Constructor for class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean

OverviewUtil - Class in net.sf.basedb.util.overview

Utility class for the overview generation functionality.

OverviewUtil() - Constructor for class net.sf.basedb.util.overview.OverviewUtil

overwrite - Variable in class net.sf.basedb.plugins.HelpImporter

overwrite - Variable in class net.sf.basedb.util.bfs.GenericExtraFileImporter

OVERWRITE - Static variable in class net.sf.basedb.core.plugin.AbstractExporterPlugin

Parameter name for the AbstractExporterPlugin.getOverwriteParameter(String, String) parameter.

OVERWRITE - Static variable in class net.sf.basedb.util.zip.AbstractFileUnpacker

The name of the parameter that asks if existing files should be overwritten or not.

OVERWRITE_ANNOTATIONS - Static variable in class net.sf.basedb.core.plugin.AbstractPlugin

The name of the parameter that asks if annotations should be overwritten or not.

overWriteParameter - Variable in class net.sf.basedb.plugins.HelpImporter

overwriteType - Static variable in class net.sf.basedb.core.plugin.AbstractExporterPlugin

ownable - Static variable in class net.sf.basedb.core.Item.DefinedPermissions

Ownable - Interface in net.sf.basedb.core

An Ownable item is an item which has a User as its owner.

ownable_annotatable - Static variable in class net.sf.basedb.core.Item.DefinedPermissions

OWNABLE_FILTER - Static variable in class net.sf.basedb.core.QueryRuntimeFilterFactory

OwnableData - Interface in net.sf.basedb.core.data

An ownable item is an item which has an owner.

OwnableFilter() - Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.OwnableFilter

ownableItems - Static variable in class net.sf.basedb.core.Metadata

OwnableUtil - Class in net.sf.basedb.core

Utility methods that will make it easier to implement the Ownable interface, including data validation.

OwnableUtil - Class in net.sf.basedb.util

OwnableUtil() - Constructor for class net.sf.basedb.core.OwnableUtil

OwnableUtil() - Constructor for class net.sf.basedb.util.OwnableUtil

OwnedData - Class in net.sf.basedb.core.data

This class extends the BasicData class and implements the OwnableData interface.

OwnedData() - Constructor for class net.sf.basedb.core.data.OwnedData

OwnedItem - Class in net.sf.basedb.core

This class inherits from the BasicItem class and implements the Ownable interface.

OwnedItem(OwnedData) - Constructor for class net.sf.basedb.core.OwnedItem

owner - Variable in class net.sf.basedb.core.data.OwnedData

ownerId - Variable in class net.sf.basedb.core.InternalJobQueue.JobRunner

ownerId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba

P

P - Variable in class net.sf.basedb.util.bcrypt.BCrypt

P_orig - Static variable in class net.sf.basedb.util.bcrypt.BCrypt

pack(String, InputStream, long, long) - Method in interface net.sf.basedb.util.zip.FilePacker

Compress the uncompressed input stream to an entry with the given name into the outputstream.

pack(String, InputStream, long, long) - Method in class net.sf.basedb.util.zip.TarFilePacker

Create a new TarEntry and write the compressed data to it.

pack(String, InputStream, long, long) - Method in class net.sf.basedb.util.zip.ZipFilePacker

Create a new entry and write the compressed data to it.

PackedFileExporter - Class in net.sf.basedb.plugins

Plug-in that packs one or more selected files and directories into a single file.

PackedFileExporter() - Constructor for class net.sf.basedb.plugins.PackedFileExporter

Create new instance.

packerParameter - Variable in class net.sf.basedb.plugins.PackedFileExporter

PackUtil - Class in net.sf.basedb.util.zip

PackUtil() - Constructor for class net.sf.basedb.util.zip.PackUtil

page - Variable in class net.sf.basedb.clients.web.taglib.Body

The parent <base:page> tag.

page - Variable in class net.sf.basedb.clients.web.taglib.Head

The parent <base:page> tag.

page - Variable in class net.sf.basedb.clients.web.taglib.Help

The parent <base:page> tag.

page - Variable in class net.sf.basedb.clients.web.taglib.HideableSection

The parent <base:page> tag.

page - Variable in class net.sf.basedb.clients.web.taglib.Icon

The parent <base:page> tag.

page - Variable in class net.sf.basedb.clients.web.taglib.table.Table

The parent <base:page> tag.

page - Variable in class net.sf.basedb.clients.web.taglib.Zoom

The parent <base:page> tag.

page - Variable in class net.sf.basedb.core.data.ContextData

page - Variable in class net.sf.basedb.core.ItemContext

Page - Class in net.sf.basedb.clients.web.taglib

This tag should be used together with the <base:head> and <base:body> tags on every JSP page in BASE.

Page() - Constructor for class net.sf.basedb.clients.web.taglib.Page

PAGE_TYPE_DEFAULT - Static variable in class net.sf.basedb.clients.web.taglib.Page

This is the default page type.

PAGE_TYPE_IFRAME - Static variable in class net.sf.basedb.clients.web.taglib.Page

The page is in a separate iframe .

PAGE_TYPE_INCLUDE - Static variable in class net.sf.basedb.clients.web.taglib.Page

This page is an included page.

PAGE_TYPE_POPUP - Static variable in class net.sf.basedb.clients.web.taglib.Page

The page is a popup dialouge.

pageContext - Variable in class net.sf.basedb.clients.web.extensions.JspContext

pageType - Variable in class net.sf.basedb.clients.web.ModeInfo

pageType - Variable in exception net.sf.basedb.clients.web.WebException

The type of page to display the error message in.

Panel - Class in net.sf.basedb.clients.web.taglib.table

This tag creates a panel in the table.

Panel() - Constructor for class net.sf.basedb.clients.web.taglib.table.Panel

parameter(String) - Static method in class net.sf.basedb.core.query.Expressions

Create an expression for a parameter without a default value or type.

parameter(String, Object) - Static method in class net.sf.basedb.core.query.Expressions

Create an expression for a parameter with a default value but no type.

parameter(String, Object, Type) - Static method in class net.sf.basedb.core.query.Expressions

Create an expression for a parameter with a default value and type.

parameter(String, Type) - Static method in class net.sf.basedb.core.query.Expressions

Create an expression for a typed parameter without a default value.

PARAMETER_DEBUG_MODE - Static variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

Parameter name for debug mode flag.

PARAMETER_EXPORTER_CLASS - Static variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

Parameter name for the class that has been selected as the exporter.

PARAMETER_EXTERNAL_CMDLINE - Static variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

Parameter name for the command line options to the external program.

PARAMETER_EXTERNAL_PARAMETERS - Static variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

Parameter name for the xml holding the parameter definitions to the external program.

PARAMETER_EXTERNAL_PATH - Static variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

Parameter name for the path to the external program.

PARAMETER_FILEFORMAT - Static variable in class net.sf.basedb.plugins.BaseFileExporterPlugin

PARAMETER_FILEFORMAT - Static variable in class net.sf.basedb.plugins.BfsExporterPlugin

PARAMETER_FILENAMEGENERATOR - Static variable in class net.sf.basedb.plugins.BfsExporterPlugin

PARAMETER_IMPORTER_CLASS - Static variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

Parameter name for the class that has been selected as the importer.

PARAMETER_NUM_CHANNELS - Static variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

Parameter name for the required number of channels.

PARAMETER_RAW_DATA_TYPE - Static variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

Parameter name for the required raw data type.

PARAMETER_REGEXP - Static variable in class net.sf.basedb.core.query.Expressions

A parameter name can only contain the characters a-z, A-Z or 0-9.

PARAMETER_SOURCE_BIOASSSAYSET - Static variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

Parameter name for the source bioassay set.

PARAMETER_SOURCE_TRANSFORM - Static variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

Parameter name for the required intensity transform of the source bioassay set.

parameterDefinition - Variable in class net.sf.basedb.plugins.executor.ProgramParameter

ParameterDefinition - Class in net.sf.basedb.plugins.executor

Represents a parameter definition for the external program.

ParameterDefinition() - Constructor for class net.sf.basedb.plugins.executor.ParameterDefinition

Create a new empty parameter definition.

ParameterException - Exception in net.sf.basedb.core

This exception is thrown by classes that uses the parameter system, ParameterType and ParameterValueData.

ParameterException(String) - Constructor for exception net.sf.basedb.core.ParameterException

Creates a new ParameterException.

ParameterExpression - Class in net.sf.basedb.core.query

Parameter expression.

ParameterExpression(String, Object, Type) - Constructor for class net.sf.basedb.core.query.ParameterExpression

parameterInfo - Variable in class net.sf.basedb.core.PluginRequest

ParameterInfo - Class in net.sf.basedb.core

Get information about a plugin configuration or parameter.

ParameterInfo(DbControl, ParameterValueData<?>) - Constructor for class net.sf.basedb.core.ParameterInfo

parameterMap - Variable in class net.sf.basedb.core.RequestInformation

parameterName - Variable in class net.sf.basedb.clients.web.plugins.ItemQueryLoader

parameterName - Variable in class net.sf.basedb.core.query.AnyToAnyRestriction

parameterOrder - Variable in class net.sf.basedb.core.AbstractSqlQuery.CountWork

parameters - Variable in class net.sf.basedb.clients.web.extensions.ServletWrapper

parameters - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload

Contains information about regular input field parameters name --> value

parameters - Variable in class net.sf.basedb.core.AbstractQuery

Parameters values added to the query.

parameters - Variable in class net.sf.basedb.core.AnnotationSimpleRestriction

parameters - Variable in class net.sf.basedb.core.data.JobData

parameters - Variable in class net.sf.basedb.core.data.ProtocolData

parameters - Variable in class net.sf.basedb.core.ParameterValuesImpl

Preloaded parameter values, if the write protected flag is set.

parameters - Variable in class net.sf.basedb.core.RequestInformation

parameters - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper

parameters - Variable in class net.sf.basedb.util.export.spotdata.BaseFileExporter

parameters - Variable in class net.sf.basedb.util.export.spotdata.BfsExporter

parameters - Variable in class net.sf.basedb.util.extensions.debug.BeanActionFactory

parameters - Variable in class net.sf.basedb.util.extensions.debug.ProxyActionFactory

parameters - Variable in class net.sf.basedb.util.QueryParameters

parameters - Variable in class net.sf.basedb.util.uri.http.HttpConnectionManager

Parameters - Class in net.sf.basedb.plugins.util

Utility class for creating some useful plug-in parameters.

Parameters() - Constructor for class net.sf.basedb.plugins.util.Parameters

ParameterType<T> - Class in net.sf.basedb.core

This is the base class for all parameter types.

ParameterType(Type, Class<T>) - Constructor for class net.sf.basedb.core.ParameterType

Creates a parameter type with no default value and allowing null values.

ParameterType(Type, Class<T>, T, boolean) - Constructor for class net.sf.basedb.core.ParameterType

Creates a new parameter type.

ParameterType(Type, Class<T>, T, boolean, int, int, int) - Constructor for class net.sf.basedb.core.ParameterType

ParameterType(Type, Class<T>, T, boolean, int, int, int, List<T>) - Constructor for class net.sf.basedb.core.ParameterType

ParameterType(Type, Class<T>, T, boolean, int, int, int, Enumeration<T, String>, boolean) - Constructor for class net.sf.basedb.core.ParameterType

parameterTypes - Variable in class net.sf.basedb.core.AnnotationBatcher.InsertBatcher

parameterTypes - Variable in class net.sf.basedb.core.AnnotationBatcher.UpdateBatcher

parameterTypes - Variable in class net.sf.basedb.core.ParameterValuesImpl

parameterTypes - Variable in class net.sf.basedb.core.ReporterCloneBatcher

ParameterValueData<T> - Class in net.sf.basedb.core.data

The base class for the different types of parameter values.

ParameterValueData() - Constructor for class net.sf.basedb.core.data.ParameterValueData

ParameterValueData(T...) - Constructor for class net.sf.basedb.core.data.ParameterValueData

ParameterValues - Interface in net.sf.basedb.core.plugin

This interface is used by the plugin to access the different parameters attached to its job and configuration.

ParameterValuesImpl - Class in net.sf.basedb.core

An implementation of the ParameterValues interface that lets a plugin write the job's configuration.

ParameterValuesImpl(Job, boolean) - Constructor for class net.sf.basedb.core.ParameterValuesImpl

ParameterValuesImpl(PluginConfiguration, int, boolean) - Constructor for class net.sf.basedb.core.ParameterValuesImpl

ParameterValuesImpl(PluginDefinition) - Constructor for class net.sf.basedb.core.ParameterValuesImpl

Empty parameter values

ParameterValuesWrapper - Class in net.sf.basedb.core.plugin

A helper class that will wrap the parameter values from one job, one configuration and one request object.

ParameterValuesWrapper(Request, ParameterValues, ParameterValues, boolean) - Constructor for class net.sf.basedb.core.plugin.ParameterValuesWrapper

parameterVersion - Variable in class net.sf.basedb.core.data.JobData

parameterVersion - Variable in class net.sf.basedb.core.data.PluginConfigurationData

parent - Variable in class net.sf.basedb.clients.web.extensions.renderer.PrefixSuffixRenderer

parent - Variable in class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator

parent - Variable in class net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult

parent - Variable in class net.sf.basedb.core.data.DirectoryData

parent - Variable in class net.sf.basedb.core.data.MeasuredBioMaterialData

parent - Variable in class net.sf.basedb.core.data.WellData

parent - Variable in class net.sf.basedb.core.plugin.NamespaceParameterValuesWrapper

parent - Variable in class net.sf.basedb.core.plugin.NamespaceRequestWrapper

parent - Variable in class net.sf.basedb.core.PluginSessionControl

parent - Variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager.AnnotationInfo

parent - Variable in class net.sf.basedb.core.QueryRuntimeFilterFactory.ChildFilter

The item type of the parent item.

parent - Variable in class net.sf.basedb.core.snapshot.DisabledInheritanceFilter

parent - Variable in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField

parent - Variable in class net.sf.basedb.plugins.batchimport.FallbackIdMethod

parent - Variable in class net.sf.basedb.plugins.BfsExporterPlugin.ExtendedExportableField

parent - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper

parent - Variable in class net.sf.basedb.util.AutoDetectFileFormat.IsImportableFilter

parent - Variable in class net.sf.basedb.util.excel.WrappedFormatter

parent - Variable in class net.sf.basedb.util.extensions.manager.filter.InstalledFilter

parent - Variable in class net.sf.basedb.util.extensions.manager.filter.ValidAndNewOrModifiedFilter

parent - Variable in class net.sf.basedb.util.filter.InverseFilter

parent - Variable in class net.sf.basedb.util.formatter.CollectionFormatter

parent - Variable in class net.sf.basedb.util.formatter.PrefixSuffixFormatter

parent - Variable in class net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser

parent - Variable in class net.sf.basedb.util.listable.CollectExtracts.ResetCollected

parent - Variable in class net.sf.basedb.util.overview.loader.AutoChildNodeLoader

parent - Variable in class net.sf.basedb.util.overview.loader.ExtensionChildNodeLoader

parent - Variable in class net.sf.basedb.util.overview.Node

parent - Variable in class net.sf.basedb.util.overview.validator.ExtensionNodeValidator

parent - Variable in class net.sf.basedb.util.parser.CropStringMapper

parent - Variable in class net.sf.basedb.util.parser.NullIfExceptionMapper

parent - Variable in class net.sf.basedb.util.PriorityComparator

parent - Variable in class net.sf.basedb.util.resources.ResourceBundleWrapper

parent - Variable in class net.sf.basedb.util.TransferRateProgressReporter

parent - Variable in class net.sf.basedb.util.Tree.Entry

PARENT_EXTRACT_MISMATCH - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if a child a raw- or derived- bioassay has a different extract than the parent bioassay.

PARENT_TO_CHILD - Enum constant in enum class net.sf.basedb.core.SyncFilter.SourceItemTransform

Source items are transformed to child items.

PARENT_TO_CHILD - Static variable in class net.sf.basedb.util.listable.ToBioSourceSourceItemTransformerFactory

PARENT_TO_CHILD - Static variable in class net.sf.basedb.util.listable.ToDerivedBioAssaySourceItemTransformerFactory

PARENT_TO_CHILD - Static variable in class net.sf.basedb.util.listable.ToExtractSourceItemTransformerFactory

PARENT_TO_CHILD - Static variable in class net.sf.basedb.util.listable.ToPhysicalBioAssaySourceItemTransformerFactory

PARENT_TO_CHILD - Static variable in class net.sf.basedb.util.listable.ToRawBioAssaySourceItemTransformerFactory

PARENT_TO_CHILD - Static variable in class net.sf.basedb.util.listable.ToSampleSourceItemTransformerFactory

ParentBioMaterialEventSourceLoader - Class in net.sf.basedb.clients.web.plugins

This is a loader implementation that load information about all source biomaterial for a given child biomaterial.

ParentBioMaterialEventSourceLoader() - Constructor for class net.sf.basedb.clients.web.plugins.ParentBioMaterialEventSourceLoader

ParentBioMaterialEventSourceLoaderFromBioAssay - Class in net.sf.basedb.clients.web.plugins

This is a loader implementation that load information about all source biomaterial for a given physical bioassay.

ParentBioMaterialEventSourceLoaderFromBioAssay() - Constructor for class net.sf.basedb.clients.web.plugins.ParentBioMaterialEventSourceLoaderFromBioAssay

ParentBioMaterialLoader - Class in net.sf.basedb.clients.web.plugins

This class get data from the parents to a MeasuredBioMaterial

ParentBioMaterialLoader(ItemQuery<? extends BioMaterial>, String) - Constructor for class net.sf.basedb.clients.web.plugins.ParentBioMaterialLoader

parentChildColumnMapping - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo

parentColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

Column mapping parameter for the parent (physical bioassay OR derived bioassay)

parentColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.SampleImporter

Column mapping parameter for the parent (biosource OR sample)

parentHasNullReporter - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo

parentHasZeroReporter - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo

parentId - Variable in class net.sf.basedb.core.data.keyring.GroupGroups

parentItem - Variable in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext

parentItem - Variable in class net.sf.basedb.util.overview.validator.ProtocolParameterValidator

parentItemNode - Variable in class net.sf.basedb.util.overview.validator.ProtocolParameterValidator

parentMapper - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

parentMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter

parentMapper - Variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter

parentMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter

parentOverride - Variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager.AnnotationInfo

parentReporterPositions - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo

parents - Variable in class net.sf.basedb.core.data.BioAssayData

parents - Variable in class net.sf.basedb.core.data.DerivedBioAssayData

parents - Variable in class net.sf.basedb.core.data.GroupData

parents - Variable in class net.sf.basedb.core.data.ItemSubtypeData

parents - Variable in class net.sf.basedb.core.data.PlateData

parents - Variable in class net.sf.basedb.util.filter.AllOfFilter

parents - Variable in class net.sf.basedb.util.filter.NoneOfFilter

parents - Variable in class net.sf.basedb.util.filter.OneOfFilter

parents - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay

parents - Variable in class net.sf.basedb.util.listable.CollectExtracts

parentSet - Variable in class net.sf.basedb.core.data.PlateData

parentSet - Variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager.AnnotationInfo

parentToChild - Variable in class net.sf.basedb.util.listable.AbstractSourceItemTransformerFactory

parentType - Variable in class net.sf.basedb.core.data.MeasuredBioMaterialData

parentTypeColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

Column mapping parameter for the parent type.

parentTypeColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.SampleImporter

Column mapping parameter for the parent type.

parentTypeMapper - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

parentTypeMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter

parentTypeMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter

parse(InputStream, String) - Method in class net.sf.basedb.util.basefile.BaseFileParser

Parse the given input stream.

parse(DbControl, Metadata, String, String, boolean, Formatter, ExcelFormatter, Formatter<Boolean>, boolean, DataLoader) - Static method in class net.sf.basedb.clients.web.plugins.ExportedProperty

parse(Item, String) - Static method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

parse(EventHandler) - Method in class net.sf.basedb.util.bfs.AnnotationParser

Parse the input stream and notify the specified event handler with events.

parse(EventHandler) - Method in class net.sf.basedb.util.bfs.DataParser

Parse the input stream and notify the specified event handler with events.

parse(EventHandler) - Method in class net.sf.basedb.util.bfs.MetadataParser

Parse the input stream and notify the specified event handler with events.

parse(EventHandler) - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser

Begin parsing and issue events to the given event handler.

parseAllExcelSheets - Variable in class net.sf.basedb.util.parser.FlatFileParser

Flag to indicate if only a single (=false) or all (=true) Excel sheets should be parsed in one go.

parseAnswer(String) - Static method in class net.sf.basedb.util.jobagent.JobAgentConnection

Utility method for parsing a 'typical' answer from a job agent.

parseAttributes(String) - Method in class net.sf.basedb.util.gtf.GtfInputStream

Parse attributes from the given template string.

parseBuildNumber(String) - Static method in class net.sf.basedb.core.Version

Find the first digits in a string and return those as the build number.

parseBytes(String, Long) - Static method in class net.sf.basedb.util.Values

Parses a string containing the number of bytes formatted as the Values.formatBytes(Long) method.

parseDate() - Method in class net.sf.basedb.util.parser.ConstantMapper

parseDate(String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Deprecated.

In 3.15, use FlatFileParser.getDateMapper(String) or FlatFileParser.getTimestampMapper(String) and Mapper.getDate(FlatFileParser.Data) instead

parsedBytes - Variable in class net.sf.basedb.util.charset.CharsetDetector

parsedCharacters - Variable in class net.sf.basedb.util.parser.FlatFileParser

The total number of parsed characters so far.

parsedDataLines - Variable in class net.sf.basedb.util.parser.FlatFileParser

The number of data lines parsed in the current section so far.

parsedFile - Variable in class net.sf.basedb.util.XmlUtil2.Validator

parsedLines - Variable in class net.sf.basedb.util.charset.CharsetDetector

parsedLines - Variable in class net.sf.basedb.util.parser.FlatFileParser

The total number of lines parsed so far.

parsedSections - Variable in class net.sf.basedb.util.parser.FlatFileParser

The number of sections parsed so far.

parseException - Variable in class net.sf.basedb.util.parser.ConstantMapper

parseHeaders() - Method in class net.sf.basedb.util.parser.FlatFileParser

Start parsing the input stream.

parseInitParameters(String) - Method in class net.sf.basedb.core.signal.SocketSignalReceiver

Parse the initialisation parameters.

parseNumeric() - Method in class net.sf.basedb.util.parser.ConstantMapper

parseParameters(String, List<String>) - Method in class net.sf.basedb.core.AbstractSqlQuery

Parse the given SQL and find named parameters.

parseQueryString(String) - Static method in class net.sf.basedb.util.QueryParameters

Parses a string in HTTP query format (key1=value1&key2=value2...) and returns it as a QueryParameters object.

parser - Variable in class net.sf.basedb.core.data.FormulaData

parser - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileImporter

parser - Variable in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser.SynchronizedData

parser - Variable in class net.sf.basedb.util.parser.ColumnMapper

parser - Variable in class net.sf.basedb.util.parser.CompoundMapper

parser - Variable in class net.sf.basedb.util.parser.ConstantMapper

parser - Variable in class net.sf.basedb.util.parser.JepMapper

Parser(int, String) - Constructor for enum class net.sf.basedb.core.Formula.Parser

parserIndex - Variable in class net.sf.basedb.util.importer.spotdata.PositionEventHandler

parsers - Variable in class net.sf.basedb.util.basefile.BaseFileParser

parserSection - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter

Section definition for grouping all file parser settings (ie. regular expressions)

parseSection(BaseFileParser, FlatFileParser) - Method in interface net.sf.basedb.util.basefile.BaseFileSectionParser

Parse the current section.

parseSection(BaseFileParser, FlatFileParser) - Method in class net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser

parseSection(BaseFileParser, FlatFileParser) - Method in class net.sf.basedb.util.importer.spotdata.SecondPassSectionSpotsParser

parseSection(BaseFileParser, FlatFileParser) - Method in class net.sf.basedb.util.importer.spotdata.SectionAssaysParser

parseSection(BaseFileParser, FlatFileParser) - Method in class net.sf.basedb.util.importer.spotdata.SectionReporterListParser

parseSimpleAnswer(String) - Static method in class net.sf.basedb.util.jobagent.JobAgentConnection

Utility method for parsing a 'typical' answer from a job agent.

parseString(String) - Method in class net.sf.basedb.clients.web.formatter.AutoItemExportFormatter

parseString(String) - Method in class net.sf.basedb.clients.web.formatter.AutoLinkFormatter

parseString(String) - Method in class net.sf.basedb.clients.web.formatter.ColorFormatter

parseString(String) - Method in class net.sf.basedb.clients.web.formatter.DataFileFormatter

Not supported

parseString(String) - Method in class net.sf.basedb.clients.web.formatter.ExtendedPropertyFormatter

parseString(String) - Method in class net.sf.basedb.clients.web.formatter.LinkedFileFormatter

parseString(String) - Method in class net.sf.basedb.clients.web.formatter.LinkedItemFormatter

parseString(String) - Method in class net.sf.basedb.clients.web.formatter.NiceFormatter

parseString(String) - Method in class net.sf.basedb.clients.web.formatter.StringFormatter

parseString(String) - Method in class net.sf.basedb.clients.web.plugins.BioMaterialEventSourceFormatter

parseString(String) - Static method in class net.sf.basedb.core.DateUtil

Parses a string to create a Date without time.

parseString(String) - Method in class net.sf.basedb.core.ExtendedProperty

Parse a string and return an object of the correct type for this property.

parseString(String) - Method in class net.sf.basedb.core.log.ChangeTypeFormatter

parseString(String) - Method in enum class net.sf.basedb.core.Type

Parse a string and return a value of the correct type.

parseString(String) - Method in class net.sf.basedb.util.export.spotdata.ExportableFieldFormatter

parseString(String) - Method in class net.sf.basedb.util.formatter.BooleanFormatter

parseString(String) - Method in class net.sf.basedb.util.formatter.CollectionFormatter

parseString(String) - Method in class net.sf.basedb.util.formatter.DateFormatter

parseString(String) - Method in class net.sf.basedb.util.formatter.EnumFormatter

parseString(String) - Method in class net.sf.basedb.util.formatter.FilePathFormatter

parseString(String) - Method in interface net.sf.basedb.util.formatter.Formatter

Parse a string and return a value of the correct type.

parseString(String) - Method in class net.sf.basedb.util.formatter.IdentifiableFormatter

parseString(String) - Method in class net.sf.basedb.util.formatter.IntegerFormatter

parseString(String) - Method in class net.sf.basedb.util.formatter.ItemTypeFormatter

parseString(String) - Method in class net.sf.basedb.util.formatter.LookupFormatter

parseString(String) - Method in class net.sf.basedb.util.formatter.MultiFormatter

parseString(String) - Method in class net.sf.basedb.util.formatter.NameableFormatter

parseString(String) - Method in class net.sf.basedb.util.formatter.NumberFormatFormatter

parseString(String) - Method in class net.sf.basedb.util.formatter.NumberFormatter

parseString(String) - Method in class net.sf.basedb.util.formatter.PrefixSuffixFormatter

parseString(String) - Method in class net.sf.basedb.util.formatter.PropertyFilterFormatter

parseString(String) - Method in class net.sf.basedb.util.formatter.ToStringFormatter

parseString(String) - Method in class net.sf.basedb.util.formatter.ValueTypeFormatter

parseString(String) - Method in class net.sf.basedb.util.formatter.WellCoordinateFormatter

parseString(String, NumberFormat, boolean) - Method in class net.sf.basedb.core.ExtendedProperty

Parse a string and return an object of the correct type for this property.

parseString(String, NumberFormat, boolean) - Method in enum class net.sf.basedb.core.Type

Parse a string and return a value of the correct type using a specific number format for numerical values, optionally ignoring unparsable numbers.

parseString(String, Formatter<Date>, boolean) - Method in enum class net.sf.basedb.core.Type

Parse a string and return a value of the correct type using a specific date format for date values, optionally ignoring unparsable dates.

parseStrings(String[]) - Method in enum class net.sf.basedb.core.Type

Parse an array of strings and try to convert them to values of the correct object type.

parseTimestamp(String) - Static method in class net.sf.basedb.core.DateUtil

Parses a string to create a Date including time.

parseToBof() - Method in class net.sf.basedb.util.bfs.AnnotationParser

Parse the header line of the annotations file.

parseToBof() - Method in class net.sf.basedb.util.bfs.DataParser

Initialize parsing of the data file.

parseToBof() - Method in class net.sf.basedb.util.bfs.MetadataParser

Parse the start of the file until the beginning-of-file marker (BFSfile) is found.

parseToBof() - Method in class net.sf.basedb.util.parser.FlatFileParser

Parse the file until the beginning-of-file marker is found.

parseToBytes() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo

parseToCsv() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo

Convert the sheet to a CSV and get an InputStream for reading the data.

parseXml(String, boolean) - Static method in class net.sf.basedb.plugins.executor.ParameterDefinition

Parse an XML document containing parameter definitions.

parsingFailure - Variable in class net.sf.basedb.util.charset.CharsetDetector

participants - Variable in class net.sf.basedb.core.data.BioPlateEventData

pass - Variable in class net.sf.basedb.util.filter.StaticFilter

password - Variable in class net.sf.basedb.clients.jobagent.Agent

password - Variable in class net.sf.basedb.core.authentication.LoginRequest

password - Variable in class net.sf.basedb.core.data.FileServerData

password - Variable in class net.sf.basedb.core.data.UserData

password - Variable in class net.sf.basedb.util.ssl.StaticKeyManager

password - Variable in class net.sf.basedb.util.uri.ConnectionParameters

password - Variable in class net.sf.basedb.util.zip.ZipFilePacker

PASSWORD - Static variable in class net.sf.basedb.core.authentication.AuthenticationMethod

This is the regular internal username/password verification authentication method.

PasswordData - Class in net.sf.basedb.core.data

This class holds the password for a user.

PasswordData() - Constructor for class net.sf.basedb.core.data.PasswordData

passwordField - Variable in class net.sf.basedb.clients.web.extensions.login.LoginFormBean

PasswordLoginFormFactory - Class in net.sf.basedb.clients.web.extensions.login

A version of the default login form that can be installed as an extension.

PasswordLoginFormFactory() - Constructor for class net.sf.basedb.clients.web.extensions.login.PasswordLoginFormFactory

PasswordParameterType - Class in net.sf.basedb.core

This class represent a parameter type that is a password (or any other type of masked string).

PasswordParameterType() - Constructor for class net.sf.basedb.core.PasswordParameterType

Create a new password parameter type, setting the max length to 255 and nulls are allowed.

PasswordParameterType(Integer, boolean) - Constructor for class net.sf.basedb.core.PasswordParameterType

Create a new password parameter type.

path - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory.PropertyPathAction

path - Variable in class net.sf.basedb.clients.web.taglib.path.PathElement

The parent Path.

path - Variable in class net.sf.basedb.core.Metadata.CombinedPropertyPath

Path - Class in net.sf.basedb.clients.web.taglib.path

This tag defines a navigation path.

Path - Class in net.sf.basedb.core

This class is used represent the path to a Directory or File item.

Path() - Constructor for class net.sf.basedb.clients.web.taglib.path.Path

Path(String, String[], String) - Constructor for class net.sf.basedb.core.Path

Create a new Path object.

Path(String, Path.Type) - Constructor for class net.sf.basedb.core.Path

Create a new Path object by parsing the given string.

Path(Path, String) - Constructor for class net.sf.basedb.core.Path

Create a new Path object.

PATH_MATCH - Static variable in class net.sf.basedb.clients.web.extensions.XJspCompiler

Path to JSP must match: /extensions/[jar-file-name]/[jsp-path].xjsp group(1) = JAR name, group(2) = JSP path

PATH_MATCH - Static variable in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter

PATH_MATCH - Static variable in class net.sf.basedb.clients.web.servlet.ExtensionsServlet

Path to servlet must match: /extensions/[jar-file-name]/[servlet-name]/optional/path/info.servlet group(1) = Servlet path; group(2) = JAR name, group(3) = Servlet name group(4) = Path info (not including .servlet)

PATH_MATCH - Static variable in class net.sf.basedb.clients.web.taglib.Head

PATH_OR_ID - Static variable in class net.sf.basedb.plugins.batchimport.FileImporter.PathIdMethod

Path.Type - Enum Class in net.sf.basedb.core

An enum that describes what type the path is

pathCanBeUsed(String, boolean) - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin

See if file path already exists and if it's allowed to overwrite it.

pathColumnMapping - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

pathColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.FileImporter

pathComparator - Static variable in class net.sf.basedb.clients.web.servlet.CompileAll

pathConverter - Variable in class net.sf.basedb.clients.web.extensions.WebClientRegisterExtensionsProcessor

PathConverter - Class in net.sf.basedb.util.extensions.xml

A value converter that can be used on all setter methods that has been annotated with the PathSetter and PathType annotations.

PathConverter() - Constructor for class net.sf.basedb.util.extensions.xml.PathConverter

Create a new empty path converter.

PathConverter(String, String) - Constructor for class net.sf.basedb.util.extensions.xml.PathConverter

Create a new initialised path converter.

PathElement - Class in net.sf.basedb.clients.web.taglib.path

This tag defines an element of a path.

PathElement() - Constructor for class net.sf.basedb.clients.web.taglib.path.PathElement

pathIdMethod - Variable in class net.sf.basedb.plugins.batchimport.FileImporter

PathIdMethod(String) - Constructor for class net.sf.basedb.plugins.batchimport.FileImporter.PathIdMethod

pathInfo - Variable in class net.sf.basedb.clients.web.extensions.RequestWrapper

PathLoader - Class in net.sf.basedb.clients.web.plugins

This is a loader implementation that load the path of a file or directory.

PathLoader() - Constructor for class net.sf.basedb.clients.web.plugins.PathLoader

pathMapper - Variable in class net.sf.basedb.plugins.batchimport.FileImporter

PathParameterType - Class in net.sf.basedb.core

This class represent a parameter type that is a path to either a directory or a file.

PathParameterType(Path.Type) - Constructor for class net.sf.basedb.core.PathParameterType

Create a new optional path parameter type.

PathParameterType(Path.Type, String, boolean) - Constructor for class net.sf.basedb.core.PathParameterType

Create a new path parameter type.

PathParameterType(Path.Type, String, boolean, int, int, int, List<String>) - Constructor for class net.sf.basedb.core.PathParameterType

paths - Variable in class net.sf.basedb.plugins.TarFileUnpacker

paths - Variable in class net.sf.basedb.util.zip.ZipUnpacker

Cache of directories.

PathSetter - Annotation Interface in net.sf.basedb.util.extensions.xml

Indicates that a factory setter method which takes a string as it's input will have the value scanned by a PathConverter before the setter method is invoked.

pathTitles - Static variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemPropertyColumn

pathToDirectory - Variable in class net.sf.basedb.plugins.batchimport.FileImporter

pathToTitle(String) - Static method in class net.sf.basedb.clients.web.extensions.list.RelatedItemPropertyColumn

Convert some paths to a more user-friendly title instead.

pathType - Variable in class net.sf.basedb.core.PathParameterType

pathType() - Element in annotation interface net.sf.basedb.util.extensions.xml.PathSetter

The type of path that should be generated.

PathType - Enum Class in net.sf.basedb.util.extensions.xml

Specify the type of paths.

PathType() - Constructor for enum class net.sf.basedb.util.extensions.xml.PathType

pattern - Variable in class net.sf.basedb.util.extensions.xml.ExtensionPointFilter

patterns - Variable in class net.sf.basedb.util.export.spotdata.AdvancedFieldConverter

pause() - Method in class net.sf.basedb.clients.jobagent.Agent

Pause the job agent.

pause(String, String, Serializable) - Method in class net.sf.basedb.core.Job

This method is used to indicate that a job has been paused, either by manual interaction or by some other trigger.

PAUSE - Enum constant in enum class net.sf.basedb.core.plugin.Response.Status

PAUSE - Static variable in class net.sf.basedb.core.signal.Signal

The PAUSE signal, that requests that the receiver should update the pause whatever it is doing and return control to the system.

pauseAgent() - Method in class net.sf.basedb.clients.jobagent.AgentController

Pause a running job agent by sending a stop request to the agents remote control service.

paused - Variable in class net.sf.basedb.util.jobagent.JobAgentInfo

PAUSED - Enum constant in enum class net.sf.basedb.core.Job.Status

The job has been paused.

PauseRequestHandler - Class in net.sf.basedb.clients.jobagent.handlers

This is a request handler for the pause command.

PauseRequestHandler(Agent) - Constructor for class net.sf.basedb.clients.jobagent.handlers.PauseRequestHandler

percent - Variable in class net.sf.basedb.core.signal.ProgressReporterSignalHandler

The current percentage status.

percent - Variable in class net.sf.basedb.core.SimpleProgressReporter

PERCENT - Static variable in class net.sf.basedb.clients.web.util.HTML

percentComplete - Variable in class net.sf.basedb.core.data.JobData

performActions(HttpServletRequest) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Perform the requested actions (install/uninstall) as given in the request form.

PerformanceTimer - Class in net.sf.basedb.util.timer

A simple timer for measuring code performance.

PerformanceTimer(String...) - Constructor for class net.sf.basedb.util.timer.PerformanceTimer

Create a new timer object for measuring one or more times.

performChange(Session) - Method in class net.sf.basedb.core.Update.DropColumnChange

performChange(Session) - Method in class net.sf.basedb.core.Update.SchemaChange

performExport(ExportOutputStream, ProgressReporter) - Method in class net.sf.basedb.clients.web.plugins.SimpleExport

performExport(ExportOutputStream, ProgressReporter) - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin

Perform the export.

performExport(ExportOutputStream, ProgressReporter) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin

performExport(ExportOutputStream, ProgressReporter) - Method in class net.sf.basedb.plugins.GalExporter

performExport(ExportOutputStream, ProgressReporter) - Method in class net.sf.basedb.plugins.HelpExporter

performExport(ExportOutputStream, ProgressReporter) - Method in class net.sf.basedb.plugins.PackedFileExporter

performExport(ExportOutputStream, ProgressReporter) - Method in class net.sf.basedb.plugins.PlateMappingExporter

performExport(ExportOutputStream, ProgressReporter) - Method in class net.sf.basedb.plugins.PluginConfigurationExporter

performExport(ProgressReporter) - Method in class net.sf.basedb.plugins.BfsExporterPlugin

performIO(DbControl, ProgressReporter) - Method in class net.sf.basedb.plugins.executor.AbstractIOSupport

Perform the IO operation.

performIO(DbControl, ProgressReporter) - Method in class net.sf.basedb.plugins.executor.BaseFileExporterSupport

performIO(DbControl, ProgressReporter) - Method in class net.sf.basedb.plugins.executor.BaseFileImporterSupport

performIO(DbControl, ProgressReporter) - Method in class net.sf.basedb.plugins.executor.BfsExporterSupport

performIO(DbControl, ProgressReporter) - Method in class net.sf.basedb.plugins.executor.BfsImporterSupport

performIO(DbControl, ProgressReporter) - Method in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport

permanent - Variable in class net.sf.basedb.core.query.QueryParameter

permanentGroups - Variable in class net.sf.basedb.core.AbstractQuery

List of permanent group expressions added to the query.

permanentHavings - Variable in class net.sf.basedb.core.AbstractQuery

List of permanent having restrictions added to the query.

permanentJoins - Variable in class net.sf.basedb.core.AbstractQuery

List of permanent joins added to the query.

permanentOrders - Variable in class net.sf.basedb.core.AbstractQuery

List of permanent orders added to the query.

permanentRestrictions - Variable in class net.sf.basedb.core.AbstractQuery

List of permanent restrictions added to the query.

permanentSelects - Variable in class net.sf.basedb.core.AbstractQuery

List of permanent selections added to the query.

permission - Variable in class net.sf.basedb.clients.web.ModeInfo

permission - Variable in class net.sf.basedb.core.AbstractEntityQuery

The logged in user's permission on the items.

permission - Variable in class net.sf.basedb.core.data.keyring.KeyPermission

permission - Variable in class net.sf.basedb.core.data.keyring.ProjectPermission

permission - Variable in class net.sf.basedb.core.ItemContext

permission - Variable in class net.sf.basedb.core.query.PermissionRestriction

Permission - Enum Class in net.sf.basedb.core

This enumeration defined constants for permissions.

Permission(int, int, String) - Constructor for enum class net.sf.basedb.core.Permission

Constructor for Permission enums.

PermissionButtonFactory - Class in net.sf.basedb.clients.web.extensions.toolbar

A button factory that can hide or disable button items based on the logged in user's permissions.

PermissionButtonFactory() - Constructor for class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

Create a new factory instance.

PermissionDeniedException - Exception in net.sf.basedb.core

This exception is thrown when trying to load or manipulate an item in the database and you don't have the required permission.

PermissionDeniedException(String) - Constructor for exception net.sf.basedb.core.PermissionDeniedException

Creates a new PermissionDeniedException.

PermissionDeniedException(String, Throwable) - Constructor for exception net.sf.basedb.core.PermissionDeniedException

Creates a new PermissionDeniedException.

PermissionDeniedException(Permission) - Constructor for exception net.sf.basedb.core.PermissionDeniedException

Creates a new PermissionDeniedException.

PermissionDeniedException(Permission, String) - Constructor for exception net.sf.basedb.core.PermissionDeniedException

Creates a new PermissionDeniedException.

permissionForKey(int, int[][]) - Method in class net.sf.basedb.core.Keyring

Returns the permission value for the specified key or PERMISSION.DENIED if not found in the array of keys.

permissionGroups - Static variable in class net.sf.basedb.clients.web.PermissionUtil

PermissionMenuItemFactory - Class in net.sf.basedb.clients.web.extensions.menu

A menu item factory that can hide or disable menu items based on the logged in user's permissions.

PermissionMenuItemFactory() - Constructor for class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

Create a new factory instance.

PermissionRestriction - Class in net.sf.basedb.core.query

Restriction that inserts an "impossible" filter requirement (1=0) if the logged in user is lacking a given permission.

PermissionRestriction(Permission, Item) - Constructor for class net.sf.basedb.core.query.PermissionRestriction

permissions - Variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl

permissions - Variable in class net.sf.basedb.core.BasicBatcher

The logged in user's permission to this item.

permissions - Variable in class net.sf.basedb.core.BasicItem

The logged in user's permission to this item.

permissions - Variable in class net.sf.basedb.core.data.PluginDefinitionData

permissions - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

permissions - Static variable in class net.sf.basedb.plugins.Base1PluginExecuter

The plug-in permissions.

permissions - Static variable in class net.sf.basedb.plugins.BaseFileExporterPlugin

permissions - Static variable in class net.sf.basedb.plugins.CdfFileReporterImporter

permissions - Static variable in class net.sf.basedb.plugins.FormulaFilter

permissions - Static variable in class net.sf.basedb.plugins.GalExporter

permissions - Static variable in class net.sf.basedb.plugins.HelpExporter

permissions - Static variable in class net.sf.basedb.plugins.HelpImporter

permissions - Static variable in class net.sf.basedb.plugins.IntensityCalculatorPlugin

permissions - Static variable in class net.sf.basedb.plugins.JepExtraValueCalculator

permissions - Static variable in class net.sf.basedb.plugins.JepIntensityTransformer

permissions - Static variable in class net.sf.basedb.plugins.LowessNormalization

permissions - Static variable in class net.sf.basedb.plugins.MedianRatioNormalization

permissions - Static variable in class net.sf.basedb.plugins.PackedFileExporter

permissions - Static variable in class net.sf.basedb.plugins.PlateFlatFileImporter

permissions - Static variable in class net.sf.basedb.plugins.PlateMappingExporter

permissions - Static variable in class net.sf.basedb.plugins.PlateMappingImporter

permissions - Static variable in class net.sf.basedb.plugins.PluginConfigurationExporter

permissions - Static variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter

permissions - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

permissions - Static variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

permissions - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

permissions - Static variable in class net.sf.basedb.util.zip.AbstractFileUnpacker

Permissions - Class in net.sf.basedb.core.plugin

This class holds permissions requested by a plugin.

Permissions(Item, Set<Permission>, Set<Permission>) - Constructor for class net.sf.basedb.core.plugin.Permissions

permissionTemplate - Variable in class net.sf.basedb.core.data.ProjectData

PermissionTemplate - Class in net.sf.basedb.core

A permission template with permissions to users, groups and projects.

PermissionTemplate(PermissionTemplateData) - Constructor for class net.sf.basedb.core.PermissionTemplate

PERMISSIONTEMPLATE - Enum constant in enum class net.sf.basedb.core.Item

The item is a PermissionTemplate.

permissionTemplateColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

PermissionTemplateData - Class in net.sf.basedb.core.data

A permission template with permissions to users, groups and projects.

PermissionTemplateData() - Constructor for class net.sf.basedb.core.data.PermissionTemplateData

permissionTemplateMapper - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

permissionTemplateQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

permissionTimeout - Static variable in class net.sf.basedb.core.Application

Number of minutes permission information can be kept in memory before it must be reloaded.

permissionTimeout() - Static method in class net.sf.basedb.core.Application

Get the maximum number of minutes permission information for a logged in user is kept in memory before beeing reloaded.

PermissionUtil - Class in net.sf.basedb.clients.web

This class is used to collect some useful methods for assigning permissions to roles and shared items.

PermissionUtil() - Constructor for class net.sf.basedb.clients.web.PermissionUtil

persist(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

persist(String, Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

phone - Variable in class net.sf.basedb.core.authentication.ExtraUserInformation

phone - Variable in class net.sf.basedb.core.data.UserData

PHYSICAL_BIOASSAY - Static variable in class net.sf.basedb.core.BioPlateEventType

The system ID for "Hybridization" event type.

PhysicalBioAssay - Class in net.sf.basedb.core

A physical bioassay is a representation of the process of performing an experiment one or more Extract:s.

PhysicalBioAssay(PhysicalBioAssayData) - Constructor for class net.sf.basedb.core.PhysicalBioAssay

PHYSICALBIOASSAY - Enum constant in enum class net.sf.basedb.core.Item

The item is a PhysicalBioAssay.

PhysicalBioAssayData - Class in net.sf.basedb.core.data

This class holds information about a physical bioassay (eg. a hybridization or similar).

PhysicalBioAssayData() - Constructor for class net.sf.basedb.core.data.PhysicalBioAssayData

PhysicalBioAssayImporter - Class in net.sf.basedb.plugins.batchimport

Plug-in for importing physical bioassays items in a batch.

PhysicalBioAssayImporter() - Constructor for class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter

PhysicalBioAssayLoader - Class in net.sf.basedb.util.overview.loader

Node loader implementation for physical bioassays.

PhysicalBioAssayLoader() - Constructor for class net.sf.basedb.util.overview.loader.PhysicalBioAssayLoader

physicalBioAssayQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

physicalBioAssays - Variable in class net.sf.basedb.core.data.DerivedBioAssayData

PhysicalBioAssayToDerivedBioAssayTransformer - Class in net.sf.basedb.util.listable

Source item transformer implementation that transform physical bioassay items to derived bioassays.

PhysicalBioAssayToDerivedBioAssayTransformer() - Constructor for class net.sf.basedb.util.listable.PhysicalBioAssayToDerivedBioAssayTransformer

Create a new physical bioassay to derived bioassay transformer.

PhysicalBioAssayToDerivedBioAssayTransformer(CollectExtracts) - Constructor for class net.sf.basedb.util.listable.PhysicalBioAssayToDerivedBioAssayTransformer

Create a new physical bioassay to derived bioassay transformer using the collected extracts to limit the returned items.

PhysicalBioAssayToExtractTransformer - Class in net.sf.basedb.util.listable

Source item transformer implementation that transform physical bioassay items to extracts.

PhysicalBioAssayToExtractTransformer() - Constructor for class net.sf.basedb.util.listable.PhysicalBioAssayToExtractTransformer

Create a new physical bioassay to extract transformer.

PhysicalBioAssayValidator - Class in net.sf.basedb.util.overview.validator

Validator implementation for physical bioassays.

PhysicalBioAssayValidator() - Constructor for class net.sf.basedb.util.overview.validator.PhysicalBioAssayValidator

ping() - Method in class net.sf.basedb.core.Application.Pinger

Ping the SessionControl by updating the last access time: SessionControl.updateLastAccess()

Pinger(SessionControl) - Constructor for class net.sf.basedb.core.Application.Pinger

pingers - Static variable in class net.sf.basedb.core.Application

pingerTask - Variable in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager

pingRemoteSlots() - Method in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager

Ping the the remote host with all active slots.

PingRequestHandler - Class in net.sf.basedb.clients.jobagent.handlers

This is a request handler for the ping command.

PingRequestHandler(Agent) - Constructor for class net.sf.basedb.clients.jobagent.handlers.PingRequestHandler

Create a new handler for the ping command.

pip - Variable in class net.sf.basedb.core.File.CharsetTesterThread

pkInfo - Variable in class net.sf.basedb.core.dbengine.TableInfo

PLACE_ON_PLATE - Static variable in class net.sf.basedb.core.BioPlateEventType

The system ID for "Place-on-plate" event type.

placeHolder - Variable in class net.sf.basedb.clients.web.extensions.login.FieldInfo

PlainTextTemplate - Class in net.sf.basedb.clients.web.plugins

A plain text template that exports data in tab-delimited format.

PlainTextTemplate(Writer, List<ExportedProperty>, Item) - Constructor for class net.sf.basedb.clients.web.plugins.PlainTextTemplate

Create a new template.

PlainTextTemplate(Writer, List<ExportedProperty>, Item, String) - Constructor for class net.sf.basedb.clients.web.plugins.PlainTextTemplate

Create a new template.

plate - Variable in class net.sf.basedb.core.data.ArrayDesignPlateData

plate - Variable in class net.sf.basedb.core.data.MappingCoordinate

The plate number.

plate - Variable in class net.sf.basedb.core.data.PlateEventData

plate - Variable in class net.sf.basedb.core.data.WellData

Plate - Class in net.sf.basedb.core

This class is represents physical plates.

Plate(PlateData) - Constructor for class net.sf.basedb.core.Plate

PLATE - Enum constant in enum class net.sf.basedb.core.Item

The item is a Plate.

PLATE - Static variable in class net.sf.basedb.core.File

The id for the FileType item representing a plate file.

PLATE_MAPPING - Static variable in class net.sf.basedb.core.File

The id for the FileType item representing a plate mapping file.

PlateCoordinate - Class in net.sf.basedb.core.data

This class defines a plate coordinate, which is row and column on a plate.

PlateCoordinate() - Constructor for class net.sf.basedb.core.data.PlateCoordinate

Create new object.

PlateCoordinate(int, int) - Constructor for class net.sf.basedb.core.data.PlateCoordinate

Create new PlateCoordinate with the specified row and column.

PlateData - Class in net.sf.basedb.core.data

This class holds information about a plate.

PlateData() - Constructor for class net.sf.basedb.core.data.PlateData

PlateEvent - Class in net.sf.basedb.core

This class represents an event in the life of a Plate.

PlateEvent(PlateEventData) - Constructor for class net.sf.basedb.core.PlateEvent

PLATEEVENT - Enum constant in enum class net.sf.basedb.core.Item

The item is a PlateEvent.

PlateEventData - Class in net.sf.basedb.core.data

This class holds information about a plate event.

PlateEventData() - Constructor for class net.sf.basedb.core.data.PlateEventData

PlateEventLogger - Class in net.sf.basedb.core.log.db

Logger for plate events that logs changes as updates to the plate the event belongs to.

PlateEventLogger(DbLogManagerFactory) - Constructor for class net.sf.basedb.core.log.db.PlateEventLogger

Creates a new plate event logger.

plateEvents - Variable in class net.sf.basedb.core.data.PlateEventTypeData

plateEventType - Variable in class net.sf.basedb.core.data.PlateEventData

PlateEventType - Class in net.sf.basedb.core

This class is used together with the PlateType class to define event types for plates.

PlateEventType(PlateEventTypeData) - Constructor for class net.sf.basedb.core.PlateEventType

PLATEEVENTTYPE - Enum constant in enum class net.sf.basedb.core.Item

The item is a PlateEventType.

PlateEventTypeData - Class in net.sf.basedb.core.data

This class holds information about a plate event type.

PlateEventTypeData() - Constructor for class net.sf.basedb.core.data.PlateEventTypeData

PlateFlatFileImporter - Class in net.sf.basedb.plugins

PlateFlatFileImporter() - Constructor for class net.sf.basedb.plugins.PlateFlatFileImporter

plateGeometry - Variable in class net.sf.basedb.core.data.BioPlateData

plateGeometry - Variable in class net.sf.basedb.core.data.PlateTypeData

PlateGeometry - Class in net.sf.basedb.core

This class defines a plate geometry, which is the number of rows and columns of wells on a Plate.

PlateGeometry(PlateGeometryData) - Constructor for class net.sf.basedb.core.PlateGeometry

PLATEGEOMETRY - Enum constant in enum class net.sf.basedb.core.Item

The item is a PlateGeometry.

plateGeometryColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter

PlateGeometryData - Class in net.sf.basedb.core.data

This class holds information about a plate geometry.

PlateGeometryData() - Constructor for class net.sf.basedb.core.data.PlateGeometryData

plateGeometryMapper - Variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter

plateMapping - Variable in class net.sf.basedb.core.data.PlateData

PlateMapping - Class in net.sf.basedb.core

This class represents a mapping from one plate geometry to another.

PlateMapping(PlateMappingData) - Constructor for class net.sf.basedb.core.PlateMapping

PLATEMAPPING - Enum constant in enum class net.sf.basedb.core.Item

The item is a PlateMapping.

PlateMappingData - Class in net.sf.basedb.core.data

This class holds information about a plate mapping.

PlateMappingData() - Constructor for class net.sf.basedb.core.data.PlateMappingData

PlateMappingExporter - Class in net.sf.basedb.plugins

Exporter for plate mappings.

PlateMappingExporter() - Constructor for class net.sf.basedb.plugins.PlateMappingExporter

Create a new importer.

PlateMappingImporter - Class in net.sf.basedb.plugins

Importer for plate mappings.

PlateMappingImporter() - Constructor for class net.sf.basedb.plugins.PlateMappingImporter

Create a new importer.

plateMappingParameter - Variable in class net.sf.basedb.plugins.PlateMappingExporter

plateNamePadding - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter

plateNamePrefix - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter

plateNamePrefixParameter - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter

plates - Variable in class net.sf.basedb.core.data.ArrayDesignData

plates - Variable in class net.sf.basedb.core.data.PlateTypeData

plates - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter

plateType - Variable in class net.sf.basedb.core.data.PlateData

plateType - Variable in class net.sf.basedb.core.data.PlateEventTypeData

plateType - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter

PlateType - Class in net.sf.basedb.core

This class represents plate types, which is a name, description, geometry and a list of event types.

PlateType(PlateTypeData) - Constructor for class net.sf.basedb.core.PlateType

PLATETYPE - Enum constant in enum class net.sf.basedb.core.Item

The item is a PlateType.

PlateTypeData - Class in net.sf.basedb.core.data

This class holds information about a plate type.

PlateTypeData() - Constructor for class net.sf.basedb.core.data.PlateTypeData

plateTypeParameter - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter

plateTypes - Variable in class net.sf.basedb.core.data.PlateGeometryData

plateTypeType - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter

platform - Variable in class net.sf.basedb.core.data.ArrayDesignData

platform - Variable in class net.sf.basedb.core.data.PlatformFileTypeData

platform - Variable in class net.sf.basedb.core.data.PlatformVariantData

platform - Variable in class net.sf.basedb.core.data.RawBioAssayData

platform - Variable in class net.sf.basedb.core.RawDataType

Platform - Class in net.sf.basedb.core

This class is used to represent an experimental platform in BASE.

Platform(PlatformData) - Constructor for class net.sf.basedb.core.Platform

Creates a new filetype item from the given data.

PLATFORM - Enum constant in enum class net.sf.basedb.core.Item

The item is a Platform

platformColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter

platformColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

PlatformData - Class in net.sf.basedb.core.data

This class hols information about experimental platforms.

PlatformData() - Constructor for class net.sf.basedb.core.data.PlatformData

PlatformFileType - Class in net.sf.basedb.core

This class represents a specific DataFileType that is part of a platform.

PlatformFileType(PlatformFileTypeData) - Constructor for class net.sf.basedb.core.PlatformFileType

Creates a new member item from the given data.

PLATFORMFILETYPE - Enum constant in enum class net.sf.basedb.core.Item

The item is a PlatformFileType

PlatformFileTypeData - Class in net.sf.basedb.core.data

This class hols information about which file types are used on which experimental platforms and variants.

PlatformFileTypeData() - Constructor for class net.sf.basedb.core.data.PlatformFileTypeData

PlatformFT(DataFileTypeData, boolean, boolean) - Constructor for class net.sf.basedb.core.Install.PlatformFT

platformId - Variable in class net.sf.basedb.core.MigrateRbaToDba.LineMapping

platformId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba

PlatformLoader - Class in net.sf.basedb.util.overview.loader

Node loader implementation for platform and platform variant.

PlatformLoader() - Constructor for class net.sf.basedb.util.overview.loader.PlatformLoader

platformMapper - Variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter

platformMapper - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

platformQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

platforms - Variable in class net.sf.basedb.core.data.DataFileTypeData

platformTypes - Static variable in class net.sf.basedb.core.RawDataTypes

PlatformValidator - Class in net.sf.basedb.util.overview.validator

Validator implementation for platforms/variants.

PlatformValidator() - Constructor for class net.sf.basedb.util.overview.validator.PlatformValidator

PlatformVariant - Class in net.sf.basedb.core

Represents variants of a Platform.

PlatformVariant(PlatformVariantData) - Constructor for class net.sf.basedb.core.PlatformVariant

Creates a new filetype item from the given data.

PLATFORMVARIANT - Enum constant in enum class net.sf.basedb.core.Item

The item is a PlatformVariant

PlatformVariantData - Class in net.sf.basedb.core.data

This class hols information about variants of experimental platforms.

PlatformVariantData() - Constructor for class net.sf.basedb.core.data.PlatformVariantData

plot - Variable in class net.sf.basedb.util.plot.HistogramPlot

plot - Variable in class net.sf.basedb.util.plot.ScatterPlot

PlotAnnotation - Class in net.sf.basedb.util.plot

Used to map spot data into different annotations.

PlotAnnotation(String, int) - Constructor for class net.sf.basedb.util.plot.PlotAnnotation

Create a new PlotAnnotation.

PlotAnnotation(String, Collection<Integer>) - Constructor for class net.sf.basedb.util.plot.PlotAnnotation

Create a new PlotAnnotation.

PlotGenerator - Interface in net.sf.basedb.clients.web.extensions.plot

Contains information about a single image in an overview plot.

PlotGeneratorBean - Class in net.sf.basedb.clients.web.extensions.plot

A simple bean-like implementation of the PlotGenerator interface.

PlotGeneratorBean() - Constructor for class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean

PlotServlet - Class in net.sf.basedb.clients.web.servlet

This servlet can plot spot data for a bioassay or bioassay set.

PlotServlet() - Constructor for class net.sf.basedb.clients.web.servlet.PlotServlet

PlotServlet.CFResultIterator - Class in net.sf.basedb.clients.web.servlet

Special implementation of a SqlResultIterator that combines the result from the parent and child into one virtual iterator.

PlotServlet.CFSqlResult - Class in net.sf.basedb.clients.web.servlet

A single result row that is combined from the parent and child results. 1 --> parent A, 2 --> parent M, 3 --> parent M - child M

plugin - Variable in class net.sf.basedb.core.data.ChangeHistoryData

plugin - Variable in class net.sf.basedb.core.ParameterValuesImpl

plugin - Variable in class net.sf.basedb.core.PluginRequest

plugin - Variable in class net.sf.basedb.util.ContextUtil.ContextResult

Plugin - Interface in net.sf.basedb.core.plugin

This interface must be implemented by all plugins to BASE.

Plugin.MainType - Enum Class in net.sf.basedb.core.plugin

pluginConfiguration - Variable in class net.sf.basedb.core.data.JobData

pluginConfiguration - Variable in class net.sf.basedb.core.PluginRequest

PluginConfiguration - Class in net.sf.basedb.core

This class is used to configure a plugin.

PluginConfiguration(PluginConfigurationData) - Constructor for class net.sf.basedb.core.PluginConfiguration

PLUGINCONFIGURATION - Enum constant in enum class net.sf.basedb.core.Item

The item is a PluginConfiguration

PluginConfigurationData - Class in net.sf.basedb.core.data

This data class is used to configure a plugin.

PluginConfigurationData() - Constructor for class net.sf.basedb.core.data.PluginConfigurationData

PluginConfigurationExporter - Class in net.sf.basedb.plugins

This plugin exports parameters of a pluginconfiguration into an XML-file.

PluginConfigurationExporter() - Constructor for class net.sf.basedb.plugins.PluginConfigurationExporter

PluginConfigurationImporter - Class in net.sf.basedb.plugins

This plugin imports pluginconfiguration from an XML-file.

PluginConfigurationImporter() - Constructor for class net.sf.basedb.plugins.PluginConfigurationImporter

pluginConfigurationList - Static variable in class net.sf.basedb.plugins.PluginConfigurationImporter

PluginConfigurationRequest - Class in net.sf.basedb.core

Configures a plugin or job.

PluginConfigurationRequest(SessionControl, InteractivePlugin, String, PluginConfiguration, ParameterValuesImpl, Job, ParameterValuesImpl, GuiContext, PluginDefinition, boolean) - Constructor for class net.sf.basedb.core.PluginConfigurationRequest

pluginDefinition - Variable in class net.sf.basedb.core.data.JobAgentSettingsData

pluginDefinition - Variable in class net.sf.basedb.core.data.JobData

pluginDefinition - Variable in class net.sf.basedb.core.data.PluginConfigurationData

pluginDefinition - Variable in class net.sf.basedb.core.PluginRequest

PluginDefinition - Class in net.sf.basedb.core

A plugin definition represents the executable plugin.

PluginDefinition(PluginDefinitionData) - Constructor for class net.sf.basedb.core.PluginDefinition

PLUGINDEFINITION - Enum constant in enum class net.sf.basedb.core.Item

The item is a PluginDefinition

PluginDefinitionData - Class in net.sf.basedb.core.data

This class represent an installed plugin.

PluginDefinitionData() - Constructor for class net.sf.basedb.core.data.PluginDefinitionData

PluginDefinitionFilter - Class in net.sf.basedb.util.extensions.xml

Filter implementation that only matches tags for plug-in definitions.

PluginDefinitionFilter() - Constructor for class net.sf.basedb.util.extensions.xml.PluginDefinitionFilter

Create a new filter.

pluginDefinitionId - Variable in class net.sf.basedb.core.data.keyring.PluginKeys

pluginDefinitions - Variable in class net.sf.basedb.util.extensions.xml.XmlLoader

pluginDirectoryParameter - Variable in class net.sf.basedb.plugins.Base1PluginExecuter

The directory where the plug-in will store it's output.

PluginExecutionRequest - Class in net.sf.basedb.core

Executes a job.

PluginExecutionRequest(PluginRequest<? extends Plugin>, String) - Constructor for class net.sf.basedb.core.PluginExecutionRequest

PluginExecutionRequest(SessionControl, Plugin, String, PluginConfiguration, ParameterValuesImpl, Job, ParameterValuesImpl, PluginDefinition) - Constructor for class net.sf.basedb.core.PluginExecutionRequest

pluginId - Variable in class net.sf.basedb.core.data.ChangeHistoryData

pluginId - Variable in class net.sf.basedb.core.Keyring

The running plugin's ID.

pluginId - Variable in class net.sf.basedb.core.log.TransactionDetails

pluginId - Variable in class net.sf.basedb.core.SessionControl

PluginInfo - Class in net.sf.basedb.util.extensions.xml

Object for holding information about a plug-in definition as it is loaded from the extensions definition file.

PluginInfo(String) - Constructor for class net.sf.basedb.util.extensions.xml.PluginInfo

Create a new information object.

PluginInfoKey - Class in net.sf.basedb.util.extensions.manager

Key implementation used to identify plug-in definitions.

PluginInfoKey(String) - Constructor for class net.sf.basedb.util.extensions.manager.PluginInfoKey

Create a new key for a plug-in with the given class name.

PluginInfoKey(PluginInfo) - Constructor for class net.sf.basedb.util.extensions.manager.PluginInfoKey

Create a new key for an plug-in definition.

PluginInstallationProcessor - Class in net.sf.basedb.util.extensions.manager.processor

File processor implementation that load and install plug-ins.

PluginInstallationProcessor(DbControl, ProcessResults) - Constructor for class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor

Create a new processor.

PluginKeys - Class in net.sf.basedb.core.data.keyring

Class for mapping the PluginKeys table.

PluginKeys() - Constructor for class net.sf.basedb.core.data.keyring.PluginKeys

Create new PluginKeys object

pluginName - Variable in class net.sf.basedb.core.log.TransactionDetails

pluginName - Variable in class net.sf.basedb.core.SessionControl

PluginParameter<T> - Class in net.sf.basedb.core

Contains information about a single parameter that the plugin needs for a request.

PluginParameter(String, String, String, ParameterType<T>) - Constructor for class net.sf.basedb.core.PluginParameter

Constructor that sets all members except the default value.

PluginParameter(String, String, String, T, ParameterType<T>) - Constructor for class net.sf.basedb.core.PluginParameter

Constructor that sets all members.

PluginPermission - Class in net.sf.basedb.core.data

PluginPermission - Class in net.sf.basedb.core

PluginPermission() - Constructor for class net.sf.basedb.core.data.PluginPermission

PluginPermission(int, int) - Constructor for class net.sf.basedb.core.data.PluginPermission

PluginPermission(int, int) - Constructor for class net.sf.basedb.core.PluginPermission

pluginPermissions - Variable in class net.sf.basedb.core.Keyring

Two-dimensional array for holding the permission for PluginDefinition:s.

PluginRequest<P extends Plugin> - Class in net.sf.basedb.core

Configures or executes a plugin.

PluginRequest(PluginRequest<? extends P>, String) - Constructor for class net.sf.basedb.core.PluginRequest

PluginRequest(SessionControl, P, String, PluginConfiguration, ParameterValuesImpl, Job, ParameterValuesImpl, PluginDefinition) - Constructor for class net.sf.basedb.core.PluginRequest

PluginRequest.RequestImpl - Class in net.sf.basedb.core

An implementation of the Request interface that is passed to the plugin.

PluginResponse - Class in net.sf.basedb.core

Get the response from a configuration step or execution of a plugin.

PluginResponse(PluginConfigurationRequest, boolean, boolean, boolean) - Constructor for class net.sf.basedb.core.PluginResponse

PluginResponse.ResponseImpl - Class in net.sf.basedb.core

An implementation of the Response interface used by the plugin to return information to the client.

plugins - Variable in class net.sf.basedb.core.data.JobAgentData

plugins - Variable in class net.sf.basedb.core.data.PluginTypeData

pluginsDir - Variable in class net.sf.basedb.clients.web.extensions.XJspCompiler

pluginsDir - Variable in class net.sf.basedb.util.extensions.manager.Settings

pluginsDirectory - Static variable in class net.sf.basedb.core.Application

The one and only place where plug-ins can be installed.

PluginSessionControl - Class in net.sf.basedb.core

This is a special session control implementation that is used for executing plugins that prevents them from logging in or out.

PluginSessionControl(String, SessionControl, PluginDefinition, Job) - Constructor for class net.sf.basedb.core.PluginSessionControl

Create a new plugin session control

PluginType - Class in net.sf.basedb.core

PluginType(PluginTypeData) - Constructor for class net.sf.basedb.core.PluginType

Creates a plugin type item.

PLUGINTYPE - Enum constant in enum class net.sf.basedb.core.Item

The item is a PluginType

PluginTypeData - Class in net.sf.basedb.core.data

This class represent an interface that a plugin can implement.

PluginTypeData() - Constructor for class net.sf.basedb.core.data.PluginTypeData

pluginTypes - Variable in class net.sf.basedb.core.data.PluginDefinitionData

pluginVersion - Variable in class net.sf.basedb.core.data.JobData

PLUS - Static variable in class net.sf.basedb.clients.web.util.HTML

pm - Variable in class net.sf.basedb.plugins.PlateMappingImporter

policy - Variable in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter

POOLING - Static variable in class net.sf.basedb.core.Protocol

The ID for the pooling protocol type, for example a protocol used when creating a biomaterial item (Sample or Extract) from a set of other biomaterial items.

pop - Variable in class net.sf.basedb.core.File.CharsetTesterThread

port - Variable in class net.sf.basedb.clients.jobagent.Agent

port - Variable in class net.sf.basedb.clients.jobagent.AgentController

port - Variable in class net.sf.basedb.core.data.JobAgentData

port - Variable in class net.sf.basedb.core.signal.SocketSignalReceiver

port - Variable in class net.sf.basedb.util.jobagent.JobAgentConnection

port - Variable in class net.sf.basedb.util.jobagent.JobAgentServerConnection

pos - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.ReporterPositions

pos - Variable in class net.sf.basedb.util.parser.ColFunction

posBatcher - Variable in class net.sf.basedb.util.importer.spotdata.PositionEventHandler

posCache - Variable in class net.sf.basedb.clients.web.ExperimentExplorer

posIndex - Variable in class net.sf.basedb.util.importer.spotdata.PositionEventHandler

position - Variable in class net.sf.basedb.clients.web.taglib.tab.TabControl

The position of the tabs.

position - Variable in class net.sf.basedb.core.data.ArrayDesignPlateData

position - Variable in class net.sf.basedb.core.data.BioMaterialEventSourceData

position - Variable in class net.sf.basedb.core.data.BioPlateData

position - Variable in class net.sf.basedb.core.data.FeatureData

position - Variable in class net.sf.basedb.core.data.RawData

position - Variable in class net.sf.basedb.core.RawDataBatcher.FeatureInfo

position - Variable in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter

position - Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData

position - Variable in class net.sf.basedb.plugins.MedianRatioNormalization.SpotData

position - Variable in class net.sf.basedb.util.overview.validator.ExtractValidator.TagPosition

POSITION - Enum constant in enum class net.sf.basedb.core.ExtraValue.CoordinateType

The extra values are attached to position coordinates only.

POSITION - Enum constant in enum class net.sf.basedb.core.FeatureIdentificationMethod

Use position number.

POSITION - Enum constant in enum class net.sf.basedb.core.VirtualTable

Table that maps position coordinates in a data cube to reporters.

POSITION - Static variable in class net.sf.basedb.core.VirtualColumn

This column stores the data cube position coordinate.

POSITION_EXTRA_FLOAT - Enum constant in enum class net.sf.basedb.core.VirtualTable

Table that stores float position extra values.

POSITION_EXTRA_INT - Enum constant in enum class net.sf.basedb.core.VirtualTable

Table that stores integer position extra values.

POSITION_EXTRA_STRING - Enum constant in enum class net.sf.basedb.core.VirtualTable

Table that stores string position extra values.

positionBatcher - Variable in class net.sf.basedb.core.DataCube

PositionBatcher - Class in net.sf.basedb.core

Batcher class for per-position data in the dynamic database.

PositionBatcher(DbControl, DataCube) - Constructor for class net.sf.basedb.core.PositionBatcher

Create a new position batcher for a data cube.

positionColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter

positionColumnMapping - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

positionColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

positionCount - Variable in class net.sf.basedb.util.IncludeExcludeFilter

PositionEventHandler - Class in net.sf.basedb.util.importer.spotdata

Event handler implementation intended to be used with a SynchronizedSpotDataParser to extract the position number from the parsed data.

PositionEventHandler(int, int, PositionBatcher, int, int) - Constructor for class net.sf.basedb.util.importer.spotdata.PositionEventHandler

Create a new event handler.

PositionExtraValueBatcher<I> - Class in net.sf.basedb.core

Batcher class for per-position extra values.

PositionExtraValueBatcher(DbControl, ExtraValue) - Constructor for class net.sf.basedb.core.PositionExtraValueBatcher

Create a new spot batcher for a bioassayset.

positionExtraValueBatchers - Variable in class net.sf.basedb.core.BioAssaySet

Cache of already created position extra value batchers.

PositionFunction - Class in net.sf.basedb.util.jep

A JEP function class that adds a pos function to a JEP expression parser.

PositionFunction() - Constructor for class net.sf.basedb.util.jep.PositionFunction

positionHandler - Variable in class net.sf.basedb.util.importer.spotdata.MatrixSpotIntensityEventHandler

positionHandler - Variable in class net.sf.basedb.util.importer.spotdata.SerialSpotIntensityEventHandler

positionIndex - Variable in class net.sf.basedb.clients.web.ExperimentExplorer

The index of the curren position on the view page.

positionIndex - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo

positionMapper - Variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter

positionMapper - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

positionMapper - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

positionSql - Variable in class net.sf.basedb.core.PositionBatcher

The statement that inserts the position/reporter link.

positionSqlStatement - Variable in class net.sf.basedb.core.PositionBatcher

The SQL string for the PositionBatcher.positionSql statement.

postDeniedItem(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.BasicNodeValidator

Submits the BasicNodeValidator.ruleDenied validator to the context as a failure unless it is null.

postDeniedItem(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.ExtensionNodeValidator

Call the same method on the parent validator and then on all extension validator actions.

postDeniedItem(DbControl, OverviewContext, Node, Node) - Method in interface net.sf.basedb.util.overview.validator.NodeValidator

Validate an item that the current user doen't have access to after a node has been created for it.

postDeniedItem(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.NullNodeValidator

Do nothing.

postFlush(Iterator) - Method in class net.sf.basedb.core.log.LoggingInterceptor

Collects all log events and sends them to the each EntityLogger.

PostgresDbEngine - Class in net.sf.basedb.core.dbengine

Database engine for Postgres.

PostgresDbEngine() - Constructor for class net.sf.basedb.core.dbengine.PostgresDbEngine

Create PostgresDbEngine.

PostgresResultWriterFactory - Class in net.sf.basedb.core.migrate.postgres

Result writer factory implementation for formatting result values suitable for importing by a PostgreSQL database.

PostgresResultWriterFactory() - Constructor for class net.sf.basedb.core.migrate.postgres.PostgresResultWriterFactory

postMissingItem(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.BasicNodeValidator

Do nothing.

postMissingItem(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.ExtensionNodeValidator

Call the same method on the parent validator and then on all extension validator actions.

postMissingItem(DbControl, OverviewContext, Node, Node) - Method in interface net.sf.basedb.util.overview.validator.NodeValidator

Validate a missing item after a node has been created for it.

postMissingItem(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.NullNodeValidator

Do nothing.

postProcessQuery(String) - Method in class net.sf.basedb.core.AbstractHqlQuery

Processes the query so that joined paths that are found in other parts of the query are replaced with the join alias.

postProcessQuery(String) - Method in class net.sf.basedb.core.AbstractQuery

Allows a subclass to modify the query.

postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.AnnotationValidator

postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.AnyToAnyValidator

postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.ArrayDesignValidator

postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.BasicNodeValidator

Do nothing.

postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.BioPlateValidator

postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.BioSourceValidator

postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.DataFileValidator

postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.DerivedBioAssayValidator

postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.ExperimentValidator

postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.ExtensionNodeValidator

Call the same method on the parent validator and then on all extension validator actions.

postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.ExtractValidator

postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.FileValidator

Checks if the file is of the correct file type.

postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.HardwareValidator

Checks if the hardware is of the correct hardware type and, if a project is active, the hardware is included as a default hardware for the project.

postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.KitValidator

Checks if the hardware is of the correct hardware type and, if a project is active, the hardware is included as a default hardware for the project.

postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.NameableNodeValidator

postValidate(DbControl, OverviewContext, Node, Node) - Method in interface net.sf.basedb.util.overview.validator.NodeValidator

Validate an existing item after a node has been created for it.

postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.NullNodeValidator

Do nothing.

postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.PhysicalBioAssayValidator

postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.PlatformValidator

Checks if the platform is the same as the default for the project.

postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.ProtocolParameterValidator

postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.ProtocolValidator

Checks if the protocol is of the correct protocol type and, if a project is active, the protocol is the same as the default for the project.

postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.RawBioAssayValidator

postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.SampleValidator

postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.SoftwareValidator

Checks if the software is of the correct software type and, if a project is active, the software is the same as the default for the project.

postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.TagValidator

Checks if the tag is of the correct subtype.

postValidateFolder(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.AnnotationValidator

postValidateFolder(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.BasicNodeValidator

Do nothing.

postValidateFolder(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.DataFileValidator

postValidateFolder(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.ExtensionNodeValidator

Call the same method on the parent validator and then on all extension validator actions.

postValidateFolder(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.ExtractValidator

If the parent is a physical bioassay, check that extracts on the same position has different tags.

postValidateFolder(DbControl, OverviewContext, Node, Node) - Method in interface net.sf.basedb.util.overview.validator.NodeValidator

Validate a folder node after all child (item-type) nodes has been added to the folder.

postValidateFolder(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.NullNodeValidator

Do nothing.

postValidateFolder(NodeFactory<I>, Node, Node, boolean) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader

postValidateFolder(Node, Node) - Method in class net.sf.basedb.util.overview.node.NodeFactory

POTENTIAL - Static variable in class net.sf.basedb.core.Quantity

The id for the Quantity object representing electrical potential.

power(String, String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine

Return POWER(<base>, <exponent>).

power(String, String) - Method in interface net.sf.basedb.core.dbengine.DbEngine

Get the function call that calculates base raised to the power of exponent For example: POW(base, value)

power(Expression, Expression) - Static method in class net.sf.basedb.core.query.Expressions

Calculate the first expression raised to the power of the second expression: new expression = e1 ^ e2

POWER - Static variable in class net.sf.basedb.core.Quantity

The id for the Quantity object representing power.

POWER_USER - Static variable in class net.sf.basedb.core.Role

The id for the Role item representing power users.

PowerExpression - Class in net.sf.basedb.core.query

Calculate the power: base ^ exponent

PowerExpression(Expression, Expression) - Constructor for class net.sf.basedb.core.query.PowerExpression

precision - Variable in class net.sf.basedb.util.formatter.AdaptiveNumberFormatter

PredefinedQuery - Class in net.sf.basedb.core

This class is used for reading XML files with information about predefined queries.

PredefinedQuery() - Constructor for class net.sf.basedb.core.PredefinedQuery

preDeniedItem(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.validator.BasicNodeValidator

preDeniedItem(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.validator.ExtensionNodeValidator

Call the same method on the parent validator and then on all extension validator actions.

preDeniedItem(DbControl, OverviewContext, Node) - Method in interface net.sf.basedb.util.overview.validator.NodeValidator

Validate an item that the current user doen't have access to before creating a node for it.

preDeniedItem(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.validator.NullNodeValidator

preferJob - Variable in class net.sf.basedb.core.plugin.ParameterValuesWrapper

prefix - Variable in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerUtil

prefix - Variable in class net.sf.basedb.clients.web.extensions.renderer.PrefixSuffixRenderer

prefix - Variable in class net.sf.basedb.clients.web.taglib.table.CellValue

prefix - Variable in class net.sf.basedb.core.query.HqlExpression

Prefix used to indentify where to put the root alias.

prefix - Variable in class net.sf.basedb.util.bfs.SequenceFilenameGenerator

prefix - Variable in class net.sf.basedb.util.formatter.PrefixSuffixFormatter

PrefixSuffixFormatter<T> - Class in net.sf.basedb.util.formatter

Formats a value with optional prefix and suffix.

PrefixSuffixFormatter(String, boolean, Formatter<T>, String, boolean) - Constructor for class net.sf.basedb.util.formatter.PrefixSuffixFormatter

Create a new formatter.

PrefixSuffixFormatter(String, Formatter<T>, String) - Constructor for class net.sf.basedb.util.formatter.PrefixSuffixFormatter

Create a new formatter.

PrefixSuffixRenderer<A extends Action> - Class in net.sf.basedb.clients.web.extensions.renderer

A wrapping renderer for HTML output that can wrap the HTML generated by a parent renderer with a prefix and/or suffix.

PrefixSuffixRenderer(JspContext, String, String) - Constructor for class net.sf.basedb.clients.web.extensions.renderer.PrefixSuffixRenderer

Create a prefix/suffix renderer that has no initial parent.

PrefixSuffixRenderer(JspContext, Renderer<? super A>, String, String) - Constructor for class net.sf.basedb.clients.web.extensions.renderer.PrefixSuffixRenderer

Create a prefix/suffix renderer with an initial parent.

preload(Restriction, Restriction) - Method in class net.sf.basedb.core.AnyToAny.FastLinkLoader

Pre-load links between source and target item type with the given link name and optionally extra restrictions for the any-to-any link and/or the target item type.

preloadAll() - Method in class net.sf.basedb.core.AnyToAny.FastLinkLoader

Pre-load all links between source and target item type with the given link name.

preloaded - Variable in class net.sf.basedb.core.RawDataBatcher

Holds info about the features of an array design.

preloadFeatures() - Method in class net.sf.basedb.core.RawDataBatcher

preMissingItem(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.validator.ArrayDesignValidator

preMissingItem(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.validator.BasicNodeValidator

Submits the BasicNodeValidator.ruleMissing validator to the context as a failure unless it is null.

preMissingItem(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.validator.DerivedBioAssayValidator

If the parent raw bioassay has a link to an extract, we ignore the missing derived bioassay.

preMissingItem(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.validator.ExtensionNodeValidator

Call the same method on the parent validator and then on all extension validator actions.

preMissingItem(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.validator.ExtractValidator

Do not report missing items if the parent node is a derived or (root) raw bioassay.

preMissingItem(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.validator.FileValidator

If the parent item has a subtype that is related to a FILE subtype, report the missing item as a Validator.MISSING_FILE failure.

preMissingItem(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.validator.HardwareValidator

If the parent item has a subtype that is related to a HARDWARE subtype, report the missing item as a Validator.MISSING_HARDWARE failure.

preMissingItem(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.validator.KitValidator

If the parent item has a subtype that is related to a KIT subtype, report the missing item as a Validator.MISSING_KIT failure.

preMissingItem(DbControl, OverviewContext, Node) - Method in interface net.sf.basedb.util.overview.validator.NodeValidator

Validate a missing item before creating a node for it.

preMissingItem(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.validator.NullNodeValidator

preMissingItem(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.validator.ProtocolValidator

If the parent item has a subtype that is related to a PROTOCOL subtype, report the missing item as a Validator.MISSING_PROTOCOL failure.

preMissingItem(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.validator.SoftwareValidator

If the parent item has a subtype that is related to a SOFTWARE subtype, report the missing item as a Validator.MISSING_SOFTWARE failure.

preMissingItem(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.validator.TagValidator

If the parent item has a subtype that is related to a TAG subtype, report the missing item as a Validator.MISSING_TAG failure.

prepare() - Method in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget

prepareActionFactory() - Method in class net.sf.basedb.util.extensions.ExtensionContext

prepareAssayIndexMap(List<BioAssay>, int, int) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

Prepare a cache that maps the bioassay column (BioAssay.getDataCubeColumnNo()) value to an index in the 'data' array this is generated.

prepareContext(JspContext) - Method in class net.sf.basedb.clients.web.extensions.AbstractJspFactory

Prepare the JSP context by adding all registered script and stylesheet references to it.

prepareContext(InvokationContext<? extends A>) - Method in class net.sf.basedb.clients.web.extensions.AbstractJspRendererFactory

If scripts and stylesheets has been added to the factory, propagates those to the JspContext.

prepareContext(InvokationContext<? extends A>) - Method in interface net.sf.basedb.util.extensions.RendererFactory

This method is called once for each request/use of an extension and should be used by a factory to initialise the context with resources that the actions may need.

prepareContext(InvokationContext<? super A>) - Method in class net.sf.basedb.clients.web.extensions.AbstractJspActionFactory

If scripts and stylesheets has been added to the factory, propagates those to the JspContext.

prepareContext(InvokationContext<? super A>) - Method in interface net.sf.basedb.util.extensions.ActionFactory

This method is called once for each request/use of an extension and have two purposes: The factory should decide if the extension should be enabled or not.

prepareContext(InvokationContext<? super ListColumnAction<Annotatable, Object>>) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumnActionFactory

We get the "columns" setting from the current ItemContext and check if there seems to be an entry for a related item.

prepareContext(InvokationContext<? super ListColumnAction<BasicItem, Object>>) - Method in class net.sf.basedb.clients.web.extensions.list.AnyLinkColumnActionFactory

We get the "columns" setting from the current ItemContext and check if there seems to be an entry for a related item.

prepareContext(InvokationContext<? super MenuItemAction>) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

prepareContext(InvokationContext<? super OverviewPlotAction>) - Method in class net.sf.basedb.clients.web.extensions.plot.MAPlotFactory

Checks if the bioassay set has 2-channel data in the database.

prepareContext(InvokationContext<? super ServiceControllerAction>) - Method in class net.sf.basedb.clients.web.extensions.service.DummyService

prepareContext(InvokationContext<? super LogManagerFactory>) - Method in class net.sf.basedb.core.log.db.DbLogManagerFactory

prepareContext(InvokationContext<? super CdfValidationAction>) - Method in class net.sf.basedb.util.affymetrix.CdfValidationFactory

prepareContext(InvokationContext<? super CelValidationAction>) - Method in class net.sf.basedb.util.affymetrix.CelValidationFactory

prepareContext(InvokationContext<? super Action>) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory

prepareContext(InvokationContext<? super Action>) - Method in class net.sf.basedb.util.extensions.debug.ProxyActionFactory

prepareContext(InvokationContext<? super GtfValidationAction>) - Method in class net.sf.basedb.util.gtf.GtfValidationFactory

prepareContext(InvokationContext<? super ValidationRuleAction>) - Method in class net.sf.basedb.util.overview.extensions.ReflectValidationRuleActionFactory

prepareContext(InvokationContext<? super ConnectionManagerFactory>) - Method in class net.sf.basedb.util.uri.http.HttpConnectionManagerActionFactory

PREPARED - Enum constant in enum class net.sf.basedb.core.Job.Status

The job is beeing prepared for execution.

prepareForCheck(InputStream) - Static method in class net.sf.basedb.util.excel.XlsxToCsvUtil

Prepare the input stream for checking with XlsxToCsvUtil.isAnExcelFile(InputStream).

prepareQuery(DbControl, ItemQuery<I>) - Method in class net.sf.basedb.plugins.batchimport.AnnotationIdMethod

Adds a restriction to the query: property = :identifier

prepareQuery(DbControl, ItemQuery<I>) - Method in class net.sf.basedb.plugins.batchimport.FallbackIdMethod

Adds a restriction to the query: property = :identifier

prepareQuery(DbControl, ItemQuery<I>) - Method in class net.sf.basedb.plugins.batchimport.FileImporter.PathIdMethod

prepareQuery(DbControl, ItemQuery<I>) - Method in interface net.sf.basedb.plugins.batchimport.IdMethod

Initialise a query to be used by this identification method.

prepareQuery(DbControl, ItemQuery<I>) - Method in class net.sf.basedb.plugins.batchimport.InternalIdMethod

Adds a restriction to the query: id = :identifier

prepareQuery(DbControl, ItemQuery<I>) - Method in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod

Adds a restriction to the query: property[0] = :identifier OR property[1] = :identifier ....

prepareQuery(DbControl, ItemQuery<I>) - Method in class net.sf.basedb.plugins.batchimport.PropertyIdMethod

Adds a restriction to the query: property = :identifier

prepareRendererFactory() - Method in class net.sf.basedb.util.extensions.ExtensionContext

prepareRendererFactory() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext

prepareRendererFactory() - Method in class net.sf.basedb.util.extensions.InvokationContext

Prepare the renderer factory if the extension or extension point has one.

Preset() - Constructor for class net.sf.basedb.core.Presets.Preset

Preset(String) - Constructor for class net.sf.basedb.core.Presets.Preset

Preset(Element) - Constructor for class net.sf.basedb.core.Presets.Preset

Load preset name and key-value pairs from XML Document.

presets - Variable in class net.sf.basedb.core.Presets

presets - Variable in class net.sf.basedb.util.extensions.manager.Settings

Presets - Class in net.sf.basedb.core

This is a generic class for handling named presets consisting of multiple key/value pairs.

Presets() - Constructor for class net.sf.basedb.core.Presets

Create a new empty presets object.

Presets.Preset - Class in net.sf.basedb.core

Represents a single preset.

PresetSelector - Class in net.sf.basedb.clients.web.taglib.table

Special tag for generating a list of saved contexts and other settings.

PresetSelector() - Constructor for class net.sf.basedb.clients.web.taglib.table.PresetSelector

presetsSetting - Static variable in class net.sf.basedb.util.overview.OverviewUtil

Name of setting to store saved presets.

PRESSURE - Static variable in class net.sf.basedb.core.Quantity

The id for the Quantity object representing pressure.

preValidate(DbControl, OverviewContext, I, Node) - Method in class net.sf.basedb.util.overview.validator.BasicNodeValidator

Subclasses should override this method if the need more validation for an existing and accessible item.

preValidate(DbControl, OverviewContext, I, Node) - Method in class net.sf.basedb.util.overview.validator.ExtensionNodeValidator

Call the same method on the parent validator and then on all extension validator actions.

preValidate(DbControl, OverviewContext, I, Node) - Method in interface net.sf.basedb.util.overview.validator.NodeValidator

Validate an existing item before creating a node for it.

preValidate(DbControl, OverviewContext, I, Node) - Method in class net.sf.basedb.util.overview.validator.NullNodeValidator

previous() - Method in class net.sf.basedb.core.ItemResultList.ResultListListIterator

previousIndex() - Method in class net.sf.basedb.core.ItemResultList.ResultListListIterator

previousState - Variable in class net.sf.basedb.core.log.EntityDetails

primary - Variable in class net.sf.basedb.core.ItemContext.PropertyFilterPair

PRIMARY - Enum constant in enum class net.sf.basedb.core.Annotation.Source

The annotation is a primary annotation.

PRIMARY - Enum constant in enum class net.sf.basedb.core.Location

The item is stored in primary storage.

PRIMARY_KEY - Static variable in class net.sf.basedb.core.VirtualColumn

Used in constructor to tell that the column is part of the primary key.

primaryCreated(int, int, int, int) - Method in class net.sf.basedb.core.ProjectSpecificAnnotationsManager

A PRIMARY annotation has been created in this transaction.

primaryKey - Variable in class net.sf.basedb.core.VirtualColumn

If the column should be part of the primary key or not.

PrimaryKeyInfo(String, Set<String>) - Constructor for class net.sf.basedb.core.dbengine.TableInfo.PrimaryKeyInfo

Create a new PrimaryKeyInfo object.

print(boolean) - Method in class net.sf.basedb.util.excel.XlsxTableWriter

print(char) - Method in class net.sf.basedb.util.excel.XlsxTableWriter

print(char[]) - Method in class net.sf.basedb.util.excel.XlsxTableWriter

print(double) - Method in class net.sf.basedb.util.excel.XlsxTableWriter

print(float) - Method in class net.sf.basedb.util.excel.XlsxTableWriter

print(int) - Method in class net.sf.basedb.util.excel.XlsxTableWriter

print(long) - Method in class net.sf.basedb.util.excel.XlsxTableWriter

print(Writer) - Method in class net.sf.basedb.util.bfs.MetadataModel

Utility method for printing the contents of this model object to a stream.

print(Object) - Method in class net.sf.basedb.util.excel.XlsxTableWriter

print(String) - Method in class net.sf.basedb.util.excel.XlsxTableWriter

PRINT_MAP - Static variable in class net.sf.basedb.core.File

The id for the FileType item representing a print map file.

PRINT_ROBOT - Static variable in class net.sf.basedb.core.Hardware

The id for the HardwareType object representing a print robot.

printHelp() - Static method in class net.sf.basedb.clients.jobagent.AgentController

PRINTING - Static variable in class net.sf.basedb.core.Protocol

The ID for the printing protocol type, for example a protocol used when printing a batch of array slides using a print robot.

println() - Method in class net.sf.basedb.util.excel.XlsxTableWriter

println(boolean) - Method in class net.sf.basedb.util.excel.XlsxTableWriter

println(char) - Method in class net.sf.basedb.util.excel.XlsxTableWriter

println(char[]) - Method in class net.sf.basedb.util.excel.XlsxTableWriter

println(double) - Method in class net.sf.basedb.util.excel.XlsxTableWriter

println(float) - Method in class net.sf.basedb.util.excel.XlsxTableWriter

println(int) - Method in class net.sf.basedb.util.excel.XlsxTableWriter

println(long) - Method in class net.sf.basedb.util.excel.XlsxTableWriter

println(Object) - Method in class net.sf.basedb.util.excel.XlsxTableWriter

println(String) - Method in class net.sf.basedb.util.excel.XlsxTableWriter

PrintMapFlatFileImporter - Class in net.sf.basedb.plugins

A plugin that imports an ArrayDesign from a printmap.

PrintMapFlatFileImporter() - Constructor for class net.sf.basedb.plugins.PrintMapFlatFileImporter

PrintMapFlatFileImporter.FormatType - Enum Class in net.sf.basedb.plugins

PrintMapFlatFileImporter.MetaBlock - Class in net.sf.basedb.plugins

PrintMapFlatFileImporter.Section - Enum Class in net.sf.basedb.plugins

printMapMember - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter

printRobot - Variable in class net.sf.basedb.core.data.ArrayBatchData

printUsage() - Static method in class net.sf.basedb.clients.jobagent.AgentController

priorities - Variable in class net.sf.basedb.clients.jobagent.Agent

The thread priority to use when executing jobs in each slot.

priorities - Variable in class net.sf.basedb.core.InternalJobQueue

The thread priority to use when executing jobs in each slot.

priority - Variable in class net.sf.basedb.core.data.JobData

priority - Variable in class net.sf.basedb.util.PriorityComparator

priorityBoost - Variable in class net.sf.basedb.core.data.JobAgentSettingsData

PriorityComparator<T> - Class in net.sf.basedb.util

A comparator implemenation that sorts a given set of objects before all other object.

PriorityComparator(Collection<T>, Comparator<? super T>) - Constructor for class net.sf.basedb.util.PriorityComparator

Create a new comparator.

PriorityComparator(SortedSet<T>) - Constructor for class net.sf.basedb.util.PriorityComparator

Create a new comparator using the same sort order as the given sorted set.

process(Annotatable) - Method in class net.sf.basedb.util.annotations.InheritAnnotationsManager

Process the given item, inheriting and/or removing annotations as specified by the rules.

processFile(ExtensionsManager, ExtensionsFile.WriteableExtensionsFile) - Method in class net.sf.basedb.clients.web.extensions.InstalledFileProcessor

processFile(ExtensionsManager, ExtensionsFile.WriteableExtensionsFile) - Method in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor

processFile(ExtensionsManager, ExtensionsFile.WriteableExtensionsFile) - Method in class net.sf.basedb.clients.web.extensions.UninstalledFileProcessor

processFile(ExtensionsManager, ExtensionsFile.WriteableExtensionsFile) - Method in class net.sf.basedb.clients.web.extensions.WebClientRegisterExtensionsProcessor

processFile(ExtensionsManager, ExtensionsFile.WriteableExtensionsFile) - Method in interface net.sf.basedb.util.extensions.manager.ExtensionsFileProcessor

Called by the extensions manager for each extensions file that it manages.

processFile(ExtensionsManager, ExtensionsFile.WriteableExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor

processFile(ExtensionsManager, ExtensionsFile.WriteableExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor

processFile(ExtensionsManager, ExtensionsFile.WriteableExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor

processFile(ExtensionsManager, ExtensionsFile.WriteableExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.processor.IgnoreFileProcessor

processFile(ExtensionsManager, ExtensionsFile.WriteableExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.processor.MarkAsProcessedProcessor

processFile(ExtensionsManager, ExtensionsFile.WriteableExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor

processFile(ExtensionsManager, ExtensionsFile.WriteableExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor

processFile(ExtensionsManager, ExtensionsFile.WriteableExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor

processFile(ExtensionsManager, ExtensionsFile.WriteableExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor

processFiles(ExtensionsFileProcessor) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager

Process all know file with the given processer.

processFiles(ExtensionsFileProcessor, Filter<ExtensionsFile>) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager

Process all known extension files with the given processor.

ProcessJobExecutor - Class in net.sf.basedb.clients.jobagent.executors

This is a job executor which starts a new process for each job to be executed.

ProcessJobExecutor() - Constructor for class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor

ProcessJobExecutor.StreamRedirector - Class in net.sf.basedb.clients.jobagent.executors

Used for redirecting standard output to a string.

ProcessResults - Class in net.sf.basedb.util.extensions.manager

Class for collecting results from a scan for new/deleted/updated extensions.

ProcessResults() - Constructor for class net.sf.basedb.util.extensions.manager.ProcessResults

Create a new process results object.

ProcessResults(ProcessResults) - Constructor for class net.sf.basedb.util.extensions.manager.ProcessResults

Create a new process results object, keeping information about previous results.

ProcessResults.FileResults - Class in net.sf.basedb.util.extensions.manager

Scan results for a single XML or JAR file.

processSignalMessage(String) - Method in class net.sf.basedb.clients.jobagent.AgentSignalReceiver

Make this method public so SignalRequestHandler can call it.

processSignalMessage(String) - Method in class net.sf.basedb.core.signal.AbstractSignalReceiver

Process a signal message.

processSignalMessage(String) - Method in class net.sf.basedb.core.signal.SocketSignalReceiver

Process the incoming message.

products - Variable in class net.sf.basedb.core.data.TransformationData

ProgramParameter - Class in net.sf.basedb.plugins.executor

A program parameter definition and it's values for a specific job.

ProgramParameter() - Constructor for class net.sf.basedb.plugins.executor.ProgramParameter

Create a new parameter object.

progress - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload

Progress information for the upload

progress - Variable in class net.sf.basedb.core.hibernate.SchemaGenerator

progress - Variable in class net.sf.basedb.core.MigrateRbaToDba

progress - Variable in class net.sf.basedb.core.Migration

progress - Variable in class net.sf.basedb.core.Migration.ProgressInputStream

progress - Variable in class net.sf.basedb.core.PluginConfigurationRequest

progress - Variable in class net.sf.basedb.core.PluginExecutionRequest

progress - Variable in class net.sf.basedb.core.SimpleProgressReporter

progress - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

progress - Variable in class net.sf.basedb.util.annotations.RunnableInheritAnnotationsManager

progress - Variable in class net.sf.basedb.util.basefile.BaseFileParser

progress - Variable in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

progress - Variable in class net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter

progress - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileImporter

progress - Variable in class net.sf.basedb.util.importer.spotdata.BfsImporter

progress - Variable in class net.sf.basedb.util.importer.spotdata.BfsImporter.ProgressEventHandler

progress - Variable in class net.sf.basedb.util.ProgressInputStream

progressDatabase - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

ProgressEventHandler(ProgressReporter, long) - Constructor for class net.sf.basedb.util.importer.spotdata.BfsImporter.ProgressEventHandler

ProgressInputStream - Class in net.sf.basedb.util

Input stream wrapper that calls a progress reporter at regular intervals.

ProgressInputStream(InputStream, AbsoluteProgressReporter) - Constructor for class net.sf.basedb.util.ProgressInputStream

Create a new input stream using the default 1MB interval.

ProgressInputStream(InputStream, AbsoluteProgressReporter, long) - Constructor for class net.sf.basedb.util.ProgressInputStream

Create a new input stream using the specified interval.

ProgressInputStream(InputStream, ProgressReporter) - Constructor for class net.sf.basedb.core.Migration.ProgressInputStream

progressParser - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

progressReport(String) - Method in class net.sf.basedb.util.ProgressInputStream

Send a progress report with the given message.

ProgressReporter - Interface in net.sf.basedb.core

Certain methods in BASE can report their progress back to the calling client application if they are giving an object that implements this interface.

ProgressReporterImpl(Job, String, String, JobAgent, ProgressReporter) - Constructor for class net.sf.basedb.core.Job.ProgressReporterImpl

ProgressReporterSignalHandler - Class in net.sf.basedb.core.signal

An implementation of a signal handler that uses a ProgressReporter to communicate signals back to the target.

ProgressReporterSignalHandler(Collection<Signal>) - Constructor for class net.sf.basedb.core.signal.ProgressReporterSignalHandler

Create a new progress reporter signal handler that supports the specified signals.

progressReportInterval - Variable in class net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser

progressReportInterval - Variable in class net.sf.basedb.util.importer.spotdata.SecondPassSectionSpotsParser

progressReportInterval - Variable in class net.sf.basedb.util.importer.spotdata.SectionReporterListParser

project - Variable in class net.sf.basedb.core.data.ChangeHistoryData

project - Variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager.AnnotationInfo

project - Variable in class net.sf.basedb.util.overview.GenericOverview

project - Variable in class net.sf.basedb.util.parser.DefaultItemFunction

Project - Class in net.sf.basedb.core

This class is used to represent projects.

Project(ProjectData) - Constructor for class net.sf.basedb.core.Project

PROJECT - Enum constant in enum class net.sf.basedb.core.Item

The item is a Project.

Project.QueryRuntimeFilterImpl - Class in net.sf.basedb.core

A runtime filter implementation that limits a query to only return projects where the logged in user is a member or owner unless the logged in user has generic read permission.

projectAnnotations - Variable in class net.sf.basedb.core.data.AnnotationTypeData

ProjectComparator(DbControl, boolean) - Constructor for class net.sf.basedb.core.snapshot.AnnotationSnapshot.ProjectComparator

ProjectData - Class in net.sf.basedb.core.data

This class holds information about a project.

ProjectData() - Constructor for class net.sf.basedb.core.data.ProjectData

projectDefaults - Variable in class net.sf.basedb.core.data.ProjectData

ProjectFilter - Class in net.sf.basedb.core.snapshot

Filter implementation that finds all annotation snapshots for a given set of projects.

ProjectFilter(Collection<Integer>) - Constructor for class net.sf.basedb.core.snapshot.ProjectFilter

Create a filter that matches the given projects ID values.

ProjectFilter(Collection<Project>, boolean) - Constructor for class net.sf.basedb.core.snapshot.ProjectFilter

Create a filter that matches the given projects and optionally default values.

ProjectFilter(DbControl) - Constructor for class net.sf.basedb.core.snapshot.ProjectFilter

Create a filter that matches all projects that the current user has access to including the default values.

projectId - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo

projectId - Variable in class net.sf.basedb.core.AnnotationBatcher

projectId - Variable in class net.sf.basedb.core.data.AnnotationData

projectId - Variable in class net.sf.basedb.core.data.annotations.AnnotationLink

projectId - Variable in class net.sf.basedb.core.data.ChangeHistoryData

projectId - Variable in class net.sf.basedb.core.data.keyring.ProjectKeys

projectId - Variable in class net.sf.basedb.core.data.keyring.ProjectPermission

projectId - Variable in class net.sf.basedb.core.FastAnnotationLoader.FastAnnotation

The ID of the project if the value is a project-specific annotation, or 0 if this is a default annotation.

projectId - Variable in class net.sf.basedb.core.FastAnnotationLoader

projectId - Variable in class net.sf.basedb.core.Keyring

The active project's ID.

projectId - Variable in class net.sf.basedb.core.log.TransactionDetails

projectId - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot

projectId - Variable in class net.sf.basedb.core.snapshot.SnapshotManager

projectKey - Variable in class net.sf.basedb.core.data.SharedData

ProjectKey - Class in net.sf.basedb.core

This class is used to get information about which projects a Shareable item has been shared to.

ProjectKey(ProjectKeyData) - Constructor for class net.sf.basedb.core.ProjectKey

PROJECTKEY - Enum constant in enum class net.sf.basedb.core.Item

The item is a ProjectKey.

ProjectKeyData - Class in net.sf.basedb.core.data

This class holds information access privileges for projects.

ProjectKeyData() - Constructor for class net.sf.basedb.core.data.ProjectKeyData

projectKeyId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba

projectKeyId - Variable in class net.sf.basedb.core.SessionControl.LoginInfo

The id of the ProjectKeyData object that new items should be shared to.

projectKeys - Variable in class net.sf.basedb.core.data.ProjectData

projectKeys - Variable in class net.sf.basedb.core.Keyring

A set holding all project keys, which is needed for efficient listing of shared items.

ProjectKeys - Class in net.sf.basedb.core.data.keyring

Class for mapping the ProjectKeys table.

ProjectKeys() - Constructor for class net.sf.basedb.core.data.keyring.ProjectKeys

Create a new ProjectKeys object.

projectKeySet - Variable in class net.sf.basedb.core.SharedItem

projectName - Variable in class net.sf.basedb.core.log.TransactionDetails

projectNames - Variable in class net.sf.basedb.core.log.TransactionDetails

ProjectPermission - Class in net.sf.basedb.core.data.keyring

Class for holding a project id and a permission value.

ProjectPermission() - Constructor for class net.sf.basedb.core.data.keyring.ProjectPermission

Create a new ProjectPermission object.

projectPermissions - Variable in class net.sf.basedb.core.Keyring

Two-dimensional array for holding the permissions for ProjectKey:s.

projectPermissions - Variable in class net.sf.basedb.core.MultiPermissions

projectPermissions - Variable in class net.sf.basedb.core.ProjectPermissions

ProjectPermissions - Class in net.sf.basedb.core

This class is used to specify permissions to share an item to projects.

ProjectPermissions() - Constructor for class net.sf.basedb.core.ProjectPermissions

Create a new empty object.

ProjectPermissions(ProjectKey) - Constructor for class net.sf.basedb.core.ProjectPermissions

Create a new object, and initialise it with the permissions from a ProjectKey.

projects - Variable in class net.sf.basedb.core.data.GroupData

projects - Variable in class net.sf.basedb.core.data.PermissionTemplateData

projects - Variable in class net.sf.basedb.core.data.ProjectKeyData

projects - Variable in class net.sf.basedb.core.data.UserData

projects - Variable in class net.sf.basedb.core.Keyring

Holds the ID and permission of all projects that the user is a member of, directly or via a group.

projects - Variable in class net.sf.basedb.core.query.SharedToRestriction

projects - Variable in class net.sf.basedb.core.snapshot.ProjectFilter

projectSpecific - Variable in class net.sf.basedb.clients.web.util.ProjectSpecificInfoFilter

ProjectSpecificAnnotationsManager - Class in net.sf.basedb.core

Internal class for keeping the "override_id" column in the "Annotations" table synchronized when annotations are creted and deleted.

ProjectSpecificAnnotationsManager(Session) - Constructor for class net.sf.basedb.core.ProjectSpecificAnnotationsManager

ProjectSpecificAnnotationsManager.AnnotationInfo - Class in net.sf.basedb.core

Holds some information about the annotation that has been created.

ProjectSpecificAnnotationsRestriction(int) - Constructor for class net.sf.basedb.core.AnnotationSet.ProjectSpecificAnnotationsRestriction

ProjectSpecificInfoFilter - Class in net.sf.basedb.clients.web.util

Helper class for finding out information about about annotation snapshots returned by AnnotationLoaderUtil.findAll(net.sf.basedb.core.snapshot.AnnotationSetSnapshot, Filter) method.

ProjectSpecificInfoFilter() - Constructor for class net.sf.basedb.clients.web.util.ProjectSpecificInfoFilter

prompt - Variable in class net.sf.basedb.clients.web.extensions.login.FieldInfo

properties - Variable in class net.sf.basedb.clients.jobagent.Agent

properties - Variable in class net.sf.basedb.clients.jobagent.AgentController

properties - Variable in class net.sf.basedb.clients.web.plugins.PlainTextTemplate

properties - Variable in class net.sf.basedb.clients.web.plugins.XlsxTemplate

properties - Variable in class net.sf.basedb.clients.web.plugins.XMLTemplate

properties - Variable in class net.sf.basedb.core.data.ReporterCloneTemplateData

properties - Variable in class net.sf.basedb.core.log.EntityDetails

properties - Variable in class net.sf.basedb.core.RawDataType

properties - Variable in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod

properties - Variable in class net.sf.basedb.util.extensions.xml.PluginInfo

property - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

property - Variable in class net.sf.basedb.clients.web.extensions.list.AnyLinkColumn

property - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

property - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

property - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemPropertyColumn

property - Variable in class net.sf.basedb.clients.web.taglib.PropertyValue

The name of the property.

property - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef

The name of the property on the item class.

property - Variable in class net.sf.basedb.clients.web.taglib.table.TableColumn

property - Variable in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter

property - Variable in class net.sf.basedb.core.MeanRawDataPropertyExpression

property - Variable in class net.sf.basedb.core.Metadata.EntityPropertyPath

property - Variable in class net.sf.basedb.core.PropertyFilter

property - Variable in class net.sf.basedb.core.query.HqlElementsExpression

property - Variable in class net.sf.basedb.core.query.HqlIndexExpression

property - Variable in class net.sf.basedb.core.query.HqlInnerJoin

property - Variable in class net.sf.basedb.core.query.HqlLeftJoin

property - Variable in class net.sf.basedb.core.query.HqlPropertyExpression

property - Variable in class net.sf.basedb.core.query.HqlRightJoin

property - Variable in class net.sf.basedb.core.query.HqlSizeExpression

property - Variable in class net.sf.basedb.core.query.ReporterListExpression

property - Variable in class net.sf.basedb.core.RawBioAssayPropertyExpression

property - Variable in class net.sf.basedb.core.RawDataPropertyExpression

property - Variable in class net.sf.basedb.core.ReporterPropertyExpression

property - Variable in class net.sf.basedb.plugins.batchimport.PropertyIdMethod

property - Variable in class net.sf.basedb.util.export.spotdata.AssayPropertyField

property(String) - Static method in class net.sf.basedb.core.query.Hql

Same as property(null, property).

property(String, String) - Static method in class net.sf.basedb.core.query.Hql

Create an expression representing a property of an object or joined alias.

property(String, String, Expression) - Static method in class net.sf.basedb.core.query.Hql

Create an expression representing the value of an indexed property.

PROPERTY - Enum constant in enum class net.sf.basedb.util.overview.node.ChildNodeDirection

Only property child nodes should be loaded.

PROPERTY_REGEXP - Static variable in class net.sf.basedb.core.query.Hql

A property can only contain the characters a-zA-Z0-9, period(.), underscore(_) or hash (#) It cannot begin or end with a period/hash and cannot have two periods/hashes in a sequence.

propertyDeleteOrders - Static variable in class net.sf.basedb.core.BatchUtil

Mapping classes/entity names to property update orders.

PropertyFilter - Class in net.sf.basedb.clients.web.taglib.table

Special tag for outputting the filter HTML that a ColumnDef has registered with the Table object.

PropertyFilter - Class in net.sf.basedb.core

Used to store filter settings in the current context.

PropertyFilter() - Constructor for class net.sf.basedb.clients.web.taglib.table.PropertyFilter

PropertyFilter(String) - Constructor for class net.sf.basedb.core.PropertyFilter

Create a new filter for a property on filter row 0.

PropertyFilter(String, int) - Constructor for class net.sf.basedb.core.PropertyFilter

Create a new filter for a property.

PropertyFilter(String, int, PropertyFilterData) - Constructor for class net.sf.basedb.core.PropertyFilter

Create a new filter from a loaded database object.

PropertyFilter(String, Operator, String, Type) - Constructor for class net.sf.basedb.core.PropertyFilter

Create a new filter for a property.

PropertyFilter(String, Operator, String, Type, boolean) - Constructor for class net.sf.basedb.core.PropertyFilter

Create a new filter for a property.

PropertyFilterData - Class in net.sf.basedb.core.data

This class holds context information to help client applications with storing common settings for tables.

PropertyFilterData() - Constructor for class net.sf.basedb.core.data.PropertyFilterData

PropertyFilterFormatter - Class in net.sf.basedb.util.formatter

Formatter for PropertyFilter items.

PropertyFilterFormatter(DbControl, Formatter<Date>) - Constructor for class net.sf.basedb.util.formatter.PropertyFilterFormatter

Create a new formatter.

PropertyFilterFormatter(DbControl, Formatter<Date>, boolean) - Constructor for class net.sf.basedb.util.formatter.PropertyFilterFormatter

Create a new formatter with option to create HTML-like tags around elements.

PropertyFilterPair() - Constructor for class net.sf.basedb.core.ItemContext.PropertyFilterPair

propertyFilters - Variable in class net.sf.basedb.core.data.ContextData

propertyFilters - Variable in class net.sf.basedb.core.data.ItemListSyncFilterData

propertyFilters - Variable in class net.sf.basedb.core.ItemContext

PropertyIdMethod - Class in net.sf.basedb.plugins.batchimport

Identification method implementation that can use a single property (eg, name, id, externalId, etc.) for identifying items.

PropertyIdMethod(String, String, String, String, boolean, Type) - Constructor for class net.sf.basedb.plugins.batchimport.PropertyIdMethod

Create a new id method.

propertyInsertOrders - Static variable in class net.sf.basedb.core.BatchUtil

Mapping classes/entity names to property insert orders.

propertyInspector - Variable in class net.sf.basedb.core.ItemContext

propertyPath - Variable in class net.sf.basedb.clients.web.plugins.AnyToAnyDataLoader

propertyPath - Variable in class net.sf.basedb.clients.web.plugins.ExportedProperty

propertyPath - Variable in class net.sf.basedb.clients.web.plugins.FileSetMemberLoader

propertyPath - Variable in class net.sf.basedb.clients.web.plugins.MapValueLoader

propertyPath - Variable in class net.sf.basedb.util.export.spotdata.AssayPropertyField

PropertyPathAction(Metadata.PropertyPath<I, V>, Metadata.PropertyPath<I, ?>) - Constructor for class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory.PropertyPathAction

PropertyPathActionFactory<I,V> - Class in net.sf.basedb.clients.web.extensions.list

A factory implementation that generates list columns based on a property path as used by the Metadata class.

PropertyPathActionFactory() - Constructor for class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

PropertyPathActionFactory.PropertyPathAction<I,V> - Class in net.sf.basedb.clients.web.extensions.list

A concrete implementation of the ListColumnAction interface.

PropertyPathProtected - Annotation Interface in net.sf.basedb.core.data

Getter methods that are annotated with this annotation should can not use Metadata.getPropertyPath to retreive their values.

propertyPathProtectedProperties - Variable in class net.sf.basedb.core.log.EntityLogOptions

propertyToColumn - Static variable in class net.sf.basedb.core.RawBioAssayPropertyExpression

propertyToColumn - Static variable in class net.sf.basedb.core.ReporterPropertyExpression

propertyToColumnCache - Static variable in class net.sf.basedb.core.RawDataPropertyExpression

propertyUpdateOrders - Static variable in class net.sf.basedb.core.BatchUtil

Mapping classes/entity names to property delete orders.

PropertyValue - Class in net.sf.basedb.clients.web.taglib

This tag is used to display the property of a BasicItem.

PropertyValue() - Constructor for class net.sf.basedb.clients.web.taglib.PropertyValue

protocol - Variable in class net.sf.basedb.core.data.ArrayBatchData

protocol - Variable in class net.sf.basedb.core.data.BioMaterialEventData

protocol - Variable in class net.sf.basedb.core.data.BioPlateEventData

protocol - Variable in class net.sf.basedb.core.data.DerivedBioAssayData

protocol - Variable in class net.sf.basedb.core.data.PlateEventData

protocol - Variable in class net.sf.basedb.core.data.RawBioAssayData

protocol - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter

Protocol - Class in net.sf.basedb.core

This class is used to represent individual protocol items and information about them.

Protocol(ProtocolData) - Constructor for class net.sf.basedb.core.Protocol

Creates a new protocol item.

PROTOCOL - Enum constant in enum class net.sf.basedb.core.Item

The item is a Protocol.

PROTOCOL - Static variable in class net.sf.basedb.core.File

The id for the FileType item representing a protocol.

protocolColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

ProtocolData - Class in net.sf.basedb.core.data

ProtocolData() - Constructor for class net.sf.basedb.core.data.ProtocolData

protocolHasBeenSet - Variable in class net.sf.basedb.core.ArrayBatch

protocolHasBeenSet - Variable in class net.sf.basedb.core.BioMaterialEvent

protocolHasBeenSet - Variable in class net.sf.basedb.core.DerivedBioAssay

protocolHasBeenSet - Variable in class net.sf.basedb.core.RawBioAssay

protocolId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba

ProtocolLoader - Class in net.sf.basedb.util.overview.loader

Node loader implementation for protocols.

ProtocolLoader() - Constructor for class net.sf.basedb.util.overview.loader.ProtocolLoader

protocolMapper - Variable in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter

protocolMapper - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

protocolMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter

protocolMapper - Variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter

protocolMapper - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

protocolMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter

protocolParameterColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

Column mapping parameter for "Protocol parameter" flag.

ProtocolParameterLoader - Class in net.sf.basedb.util.overview.loader

Node loader implementation for protocol parameters.

ProtocolParameterLoader() - Constructor for class net.sf.basedb.util.overview.loader.ProtocolParameterLoader

protocolParameterMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

ProtocolParameterValidator - Class in net.sf.basedb.util.overview.validator

Validator implementation for protocol parameters.

ProtocolParameterValidator() - Constructor for class net.sf.basedb.util.overview.validator.ProtocolParameterValidator

protocolQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

protocols - Variable in class net.sf.basedb.core.data.AnnotationTypeData

protocolType - Variable in class net.sf.basedb.core.data.PlateEventTypeData

ProtocolValidator - Class in net.sf.basedb.util.overview.validator

Validator implementation for protocols.

ProtocolValidator() - Constructor for class net.sf.basedb.util.overview.validator.ProtocolValidator

proxy - Variable in class net.sf.basedb.core.signal.SocketSignalReceiver

proxy - Variable in class net.sf.basedb.core.Trashcan.CircularRefInfo

proxy - Variable in class net.sf.basedb.util.extensions.debug.ProxyActionFactory

ProxyActionFactory - Class in net.sf.basedb.util.extensions.debug

Generic action factory class that can generate instances of actions if the action class is an interface.

ProxyActionFactory() - Constructor for class net.sf.basedb.util.extensions.debug.ProxyActionFactory

Creates a new proxy factory.

proxyLoaders - Variable in class net.sf.basedb.util.JarClassLoader

Class loaders for extensions.

ps - Variable in class net.sf.basedb.core.QueryExecutor.FutureResultSet

ps - Variable in class net.sf.basedb.core.QueryExecutor.FutureUpdate

pspManager - Variable in class net.sf.basedb.core.DbControl

publication - Variable in class net.sf.basedb.core.data.ExperimentData

publicationDate - Variable in class net.sf.basedb.core.data.ExperimentData

pubMedId - Variable in class net.sf.basedb.core.data.ExperimentData

pushAnnotations - Variable in class net.sf.basedb.core.data.ItemSubtypeData

pushOnly - Variable in class net.sf.basedb.util.listable.ExtractToChildExtractTransformer

pushOnly - Variable in class net.sf.basedb.util.listable.ExtractToParentExtractTransformer

pushOnly - Variable in class net.sf.basedb.util.listable.ExtractToSampleTransformer

pushOnly - Variable in class net.sf.basedb.util.listable.SampleToBioSourceTransformer

pushOnly - Variable in class net.sf.basedb.util.listable.SampleToChildSampleTransformer

pushOnly - Variable in class net.sf.basedb.util.listable.SampleToParentSampleTransformer

PushToParentsTransformer - Class in net.sf.basedb.util.listable

Transformer implementation that can be used to to find parent items to children that have a subtype with the "push annotations to parent" flag set.

PushToParentsTransformer(Item) - Constructor for class net.sf.basedb.util.listable.PushToParentsTransformer

put(AnnotationUtil.AnnotatableWrapper, Set<AnnotationUtil.AnnotatableWrapper>) - Method in class net.sf.basedb.util.AnnotationUtil.Cache

put(T, String) - Method in class net.sf.basedb.util.formatter.LookupFormatter

Add a lookup key/value pair.

putAll(Map<? extends T, ? extends String>) - Method in class net.sf.basedb.util.formatter.LookupFormatter

Copy multiple lookup key/value pairs from a map

putAll(Enumeration<? extends T, ? extends String>) - Method in class net.sf.basedb.util.formatter.LookupFormatter

Copy multiple lookup key/value pairs from an enumeration.

putNextEntry(TarEntry, TarOutputStream) - Static method in class net.sf.basedb.util.zip.TarUtil

Put the next entry to a TAR stream.

putNode(K, Node) - Method in class net.sf.basedb.util.overview.cache.NodeCache

Q

QUADRATIC_MEAN - Enum constant in enum class net.sf.basedb.core.Formula.AverageMethod

quadraticMean(Expression) - Static method in class net.sf.basedb.core.query.Aggregations

Calculates the quadratic mean, also called Root Mean Square, for an expression: new expression = sqrt(AVG(e*e))

QuadraticMeanExpression - Class in net.sf.basedb.core.query

Calculates the quadratic mean of an expression

QuadraticMeanExpression(Expression) - Constructor for class net.sf.basedb.core.query.QuadraticMeanExpression

quantity - Variable in class net.sf.basedb.core.data.AnnotationTypeData

quantity - Variable in class net.sf.basedb.core.data.UnitData

quantity - Variable in class net.sf.basedb.core.data.UnitSymbolData

Quantity - Class in net.sf.basedb.core

This class is used to represent a quantity for specifying units to annotations.

Quantity(QuantityData) - Constructor for class net.sf.basedb.core.Quantity

Creates a quantity item.

QUANTITY - Enum constant in enum class net.sf.basedb.core.Item

The item is a Quantity.

QuantityData - Class in net.sf.basedb.core.data

This class holds information quantities.

QuantityData() - Constructor for class net.sf.basedb.core.data.QuantityData

quantityId - Variable in class net.sf.basedb.util.units.UnitCache.CacheKey

queries - Variable in class net.sf.basedb.util.query.MultiQueryIterator

query - Variable in class net.sf.basedb.clients.web.plugins.DataQueryWrapper

query - Variable in class net.sf.basedb.clients.web.plugins.DynamicQueryWrapper

query - Variable in class net.sf.basedb.clients.web.plugins.ItemQueryLoader

query - Variable in class net.sf.basedb.clients.web.plugins.ItemQueryWrapper

query - Variable in class net.sf.basedb.clients.web.plugins.ParentBioMaterialEventSourceLoader

query - Variable in class net.sf.basedb.clients.web.plugins.ParentBioMaterialEventSourceLoaderFromBioAssay

query - Variable in class net.sf.basedb.clients.web.plugins.PathLoader

query - Variable in class net.sf.basedb.clients.web.plugins.ReporterScoreQueryWrapper

query - Variable in class net.sf.basedb.core.hibernate.NativeQueryWrapper

query - Variable in class net.sf.basedb.core.hibernate.QueryWrapper

query - Variable in class net.sf.basedb.core.ItemContext

query - Variable in class net.sf.basedb.core.QueryExecutor.FutureItem

query - Variable in class net.sf.basedb.core.QueryExecutor.FutureScrollIterator

query - Variable in class net.sf.basedb.util.listable.RestrictionTransformer

query - Variable in class net.sf.basedb.util.units.UnitCache

Query - Interface in net.sf.basedb.core.query

This defines the simplest form of a relational query.

QueryElement - Interface in net.sf.basedb.core.query

A query element is used in various places in a Query to build the structure of the query.

QueryExecutor - Class in net.sf.basedb.core

Utility class for executing SQL and Hibernate queries.

QueryExecutor() - Constructor for class net.sf.basedb.core.QueryExecutor

QueryExecutor.Cancelable - Interface in net.sf.basedb.core

Interface to be implemented by classes that knows how to cancel a query.

QueryExecutor.CancelableSession - Class in net.sf.basedb.core

Cancels the query running in a Hibernate session.

QueryExecutor.CancelableStatelessSession - Class in net.sf.basedb.core

Cancels a query running in a stateless Hibernate session.

QueryExecutor.CancelableStatement - Class in net.sf.basedb.core

Cancels a statement by calling Statement.cancel().

QueryExecutor.FutureItem<T> - Class in net.sf.basedb.core

QueryExecutor.FutureResultSet - Class in net.sf.basedb.core

A callable implementation the calls PreparedStatement.executeQuery()

QueryExecutor.FutureScrollIterator<T> - Class in net.sf.basedb.core

Calls Query.scroll(ScrollMode) and returns the result as a ScrollIterator.

QueryExecutor.FutureUpdate - Class in net.sf.basedb.core

A callable implementation the calls PreparedStatement.executeUpdate()

queryFile - Static variable in class net.sf.basedb.core.Application

The path to the file containing predefined queries.

QueryFilterAction - Interface in net.sf.basedb.core.query

Actions for creating restrictions on queries.

QueryParameter - Class in net.sf.basedb.core.query

Holds information (name, type and value) about a single parameter to a query.

QueryParameter(String) - Constructor for class net.sf.basedb.core.query.QueryParameter

Create a new empty non-permanent query parameter.

QueryParameter(String, boolean, Type, Object) - Constructor for class net.sf.basedb.core.query.QueryParameter

Create a new query parameter.

QueryParameters - Class in net.sf.basedb.util

Utiltity class for parsing string values in the form of HTTP request query parameters:

QueryParameters(String) - Constructor for class net.sf.basedb.util.QueryParameters

QueryRestrictions() - Constructor for class net.sf.basedb.core.ItemContext.QueryRestrictions

QueryResult - Interface in net.sf.basedb.core.query

This is the root interface for query results.

QueryRuntimeFilter - Interface in net.sf.basedb.core

Represents a filter that is applied to a query just before it is executed in order to limit the result.

QueryRuntimeFilterFactory - Class in net.sf.basedb.core

This is a factory class for QueryRuntimeFilter implementations.

QueryRuntimeFilterFactory() - Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory

QueryRuntimeFilterFactory.AnnotatableFilter - Class in net.sf.basedb.core

A required filter for Annotatable items.

QueryRuntimeFilterFactory.BasicFilter - Class in net.sf.basedb.core

An optional default filter for BasicItem:s that are not Ownable or Shareable.

QueryRuntimeFilterFactory.ChainedFilter - Class in net.sf.basedb.core

Chains one or more filters into a single filter.

QueryRuntimeFilterFactory.ChildFilter - Class in net.sf.basedb.core

An optional filter that can be used by BasicItem:s to replace the QueryRuntimeFilterFactory.BasicFilter.

QueryRuntimeFilterFactory.DenyAllFilter - Class in net.sf.basedb.core

A required filter for all items, which checks if the logged in user has been "granted" the Permission.DENIED permission for a specific item type.

QueryRuntimeFilterFactory.OwnableFilter - Class in net.sf.basedb.core

An optional default filter for Ownable items that are not Shareable.

QueryRuntimeFilterFactory.RemovableFilter - Class in net.sf.basedb.core

A required filter for Removable items.

QueryRuntimeFilterFactory.ShareableFilter - Class in net.sf.basedb.core

An optional default filter for Shareable items.

QueryRuntimeFilterImpl() - Constructor for class net.sf.basedb.core.Annotation.QueryRuntimeFilterImpl

QueryRuntimeFilterImpl() - Constructor for class net.sf.basedb.core.AnnotationSet.QueryRuntimeFilterImpl

QueryRuntimeFilterImpl() - Constructor for class net.sf.basedb.core.FileSet.QueryRuntimeFilterImpl

QueryRuntimeFilterImpl() - Constructor for class net.sf.basedb.core.FileSetMember.QueryRuntimeFilterImpl

QueryRuntimeFilterImpl() - Constructor for class net.sf.basedb.core.Group.QueryRuntimeFilterImpl

QueryRuntimeFilterImpl() - Constructor for class net.sf.basedb.core.Message.QueryRuntimeFilterImpl

QueryRuntimeFilterImpl() - Constructor for class net.sf.basedb.core.News.QueryRuntimeFilterImpl

QueryRuntimeFilterImpl() - Constructor for class net.sf.basedb.core.Project.QueryRuntimeFilterImpl

QueryRuntimeFilterImpl() - Constructor for class net.sf.basedb.core.Quota.QueryRuntimeFilterImpl

QueryRuntimeFilterImpl() - Constructor for class net.sf.basedb.core.Role.QueryRuntimeFilterImpl

QueryRuntimeFilterImpl() - Constructor for class net.sf.basedb.core.Session.QueryRuntimeFilterImpl

QueryRuntimeFilterImpl() - Constructor for class net.sf.basedb.core.User.QueryRuntimeFilterImpl

QueryRuntimeFilterImpl() - Constructor for class net.sf.basedb.core.UserDevice.QueryRuntimeFilterImpl

QueryRuntimeFilterManager - Class in net.sf.basedb.core

This class manages the enabling/disabling of QueryRuntimeFilter:s.

QueryRuntimeFilterManager(DbControl, Item) - Constructor for class net.sf.basedb.core.QueryRuntimeFilterManager

Create a new manager for the DbControl.

querySection - Variable in class net.sf.basedb.core.AbstractQuery

The section of the query that is currently beeing built.

QuerySection - Enum Class in net.sf.basedb.core.query

Indicates which part of a query that is currently beeing built.

QuerySection() - Constructor for enum class net.sf.basedb.core.query.QuerySection

QueryType - Enum Class in net.sf.basedb.core.query

A type representing the language of the query.

QueryType() - Constructor for enum class net.sf.basedb.core.query.QueryType

QueryWrapper<R> - Class in net.sf.basedb.core.hibernate

A simple wrapper around hibernate queries which simply forwards all calls to a parent query.

QueryWrapper<T> - Interface in net.sf.basedb.clients.web.plugins

A helper interface for the SimpleExport class to make it easier to interact with different types of queries.

QueryWrapper(Query<R>) - Constructor for class net.sf.basedb.core.hibernate.QueryWrapper

queue - Variable in class net.sf.basedb.core.ItemList.DelayedAdditionManager

queue() - Method in class net.sf.basedb.core.ItemList.DelayedAdditionManager

queuedInsertCount - Variable in class net.sf.basedb.core.FilterBatcher

The number of queued inserts.

queuedInsertCount - Variable in class net.sf.basedb.core.MappingBatcher

The number of queued inserts.

queuedInsertCount - Variable in class net.sf.basedb.core.PositionBatcher

The number of queued inserts.

queuedInsertCount - Variable in class net.sf.basedb.core.PositionExtraValueBatcher

The number of queued inserts.

queuedInsertCount - Variable in class net.sf.basedb.core.SpotBatcher

The number of queued inserts.

queuedInsertCount - Variable in class net.sf.basedb.core.SpotExtraValueBatcher

The number of queued inserts.

quota - Variable in class net.sf.basedb.core.data.GroupData

quota - Variable in class net.sf.basedb.core.data.UserData

Quota - Class in net.sf.basedb.core

This class is used to represent disk quota settings for users and groups.

Quota(QuotaData) - Constructor for class net.sf.basedb.core.Quota

Create a new Quota item.

QUOTA - Enum constant in enum class net.sf.basedb.core.Item

The item is a Quota.

Quota.QueryRuntimeFilterImpl - Class in net.sf.basedb.core

A runtime filter implementation that limits a query to only return the quota assigned to the logged in user unless the logged in user has generic read permission.

QuotaData - Class in net.sf.basedb.core.data

This file holds information about a qouta.

QuotaData() - Constructor for class net.sf.basedb.core.data.QuotaData

QuotaException - Exception in net.sf.basedb.core

This exception is thrown to signal that the user's quota has been exceeded and that an DiskConsumable item cannot be saved.

QuotaException() - Constructor for exception net.sf.basedb.core.QuotaException

Create a new QuotaException object.

QuotaException(Location, QuotaTypeData, long, long) - Constructor for exception net.sf.basedb.core.QuotaException

Create a new QuotaException object.

quotaGroup - Variable in class net.sf.basedb.core.data.UserData

QuotaIndex - Class in net.sf.basedb.core.data

This is a helper class for the QuotaData item to help with the Hibernate mapping between quota and quota type/location/max bytes.

QuotaIndex() - Constructor for class net.sf.basedb.core.data.QuotaIndex

QuotaIndex(QuotaTypeData, int) - Constructor for class net.sf.basedb.core.data.QuotaIndex

quotaLimited - Variable in enum class net.sf.basedb.core.Location

If this location is limited by quota.

quotaType - Variable in class net.sf.basedb.core.data.DiskUsageData

quotaType - Variable in class net.sf.basedb.core.data.QuotaIndex

QuotaType - Class in net.sf.basedb.core

This class represents the different types a quota can have.

QuotaType(QuotaTypeData) - Constructor for class net.sf.basedb.core.QuotaType

Creates a new QuotaType item.

QUOTATYPE - Enum constant in enum class net.sf.basedb.core.Item

The item is a QuotaType.

QuotaTypeData - Class in net.sf.basedb.core.data

This class holds information about different QuotaTypes.

QuotaTypeData() - Constructor for class net.sf.basedb.core.data.QuotaTypeData

quotaTypes - Variable in class net.sf.basedb.core.DiskUsageStatistics

quotaValues - Variable in class net.sf.basedb.core.data.QuotaData

quote(String) - Static method in class net.sf.basedb.core.HibernateUtil

Quote a string with the default quote type for the current database engine.

QUOTE - Static variable in class net.sf.basedb.clients.web.util.HTML

R

r - Variable in class net.sf.basedb.core.query.BooleanExpression

r - Variable in class net.sf.basedb.core.query.NotRestriction

r - Variable in class net.sf.basedb.util.basefile.BaseFileWriter

RADIOACTIVITY - Static variable in class net.sf.basedb.core.Quantity

The id for the Quantity object representing radioactivity.

rangeMidMax - Variable in class net.sf.basedb.util.ColorGenerator

The inverted difference between the max and mid values: 1 / (maxValue - midValue)

rangeMinMid - Variable in class net.sf.basedb.util.ColorGenerator

The inverted difference between the mid and min values: 1 / (midValue - minValue)

rangeRange - Variable in class net.sf.basedb.util.plot.HistogramPlot

raw - Variable in class net.sf.basedb.util.IntensityCalculatorUtil.JepIntensityCalculatorImpl

raw(String) - Method in class net.sf.basedb.util.jep.RawFunction

Get the value of the specified property of the current raw data object.

raw(String) - Method in class net.sf.basedb.util.jep.ReporterFunction

Get the value of the specified property of the current raw data object.

RAW - Enum constant in enum class net.sf.basedb.core.ReporterCloneBatcher.CloneSource

Use the raw data for all raw bioassays in the experiment as the source for reporters.

RAW_DATA - Static variable in class net.sf.basedb.core.File

The id for the FileType item representing a raw data file.

RAW_DATA - Static variable in class net.sf.basedb.core.QuotaType

The ID for the raw data.

rawBioAssay - Variable in class net.sf.basedb.core.data.RawData

rawBioAssay - Variable in class net.sf.basedb.core.data.RootRawBioAssayData

rawBioAssay - Variable in class net.sf.basedb.core.DynamicRawDataQuery

rawBioAssay - Variable in class net.sf.basedb.core.RawDataBatcher

The raw bioassay this batcher adds raw data to.

rawBioAssay - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

rawBioAssay - Variable in class net.sf.basedb.util.jep.MeanFunction

rawBioAssay(String) - Static method in class net.sf.basedb.core.query.Dynamic

Create an expression representing a property of a raw bioassay.

RawBioAssay - Class in net.sf.basedb.core

A rawbioassay represents the raw data generated from a single DerivedBioAssay.

RawBioAssay(RawBioAssayData) - Constructor for class net.sf.basedb.core.RawBioAssay

RAWBIOASSAY - Enum constant in enum class net.sf.basedb.core.Item

The item is a RawBioAssay.

RAWBIOASSAY_ID - Static variable in class net.sf.basedb.core.VirtualColumn

This column stores the id of a raw bioassay.

rawBioAssayData - Variable in class net.sf.basedb.core.RawDataBatcher

Just a copy of the data object for the raw bioassay.

RawBioAssayData - Class in net.sf.basedb.core.data

This class holds information about a raw bioassay, which is the raw data extracted from a scan.

RawBioAssayData() - Constructor for class net.sf.basedb.core.data.RawBioAssayData

RawBioAssayImporter - Class in net.sf.basedb.plugins.batchimport

Plug-in for importing raw bioassay items in a batch.

RawBioAssayImporter() - Constructor for class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

RawBioAssayJoiner(JoinType) - Constructor for class net.sf.basedb.core.DynamicRawDataQuery.RawBioAssayJoiner

RawBioAssayLoader - Class in net.sf.basedb.util.overview.loader

Node loader implementation for raw bioassays.

RawBioAssayLoader() - Constructor for class net.sf.basedb.util.overview.loader.RawBioAssayLoader

RawBioAssayPropertyExpression - Class in net.sf.basedb.core

An expression representing the property of a raw bioassay.

RawBioAssayPropertyExpression(String) - Constructor for class net.sf.basedb.core.RawBioAssayPropertyExpression

Create a new raw bioassay property expression.

rawBioAssays - Variable in class net.sf.basedb.core.data.DerivedBioAssayData

rawBioAssays - Variable in class net.sf.basedb.core.data.ExperimentData

rawBioAssays - Variable in class net.sf.basedb.core.data.ExtractData

rawBioAssays - Variable in class net.sf.basedb.core.data.JobData

rawBioAssays - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter

rawBioAssays - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter.FileIterator

RAWBIOASSAYS - Static variable in class net.sf.basedb.core.RealTable

rawBioAssaysParameter - Variable in class net.sf.basedb.plugins.IntensityCalculatorPlugin

rawBioAssaysType - Variable in class net.sf.basedb.plugins.IntensityCalculatorPlugin

RawBioAssayToDerivedBioAssayTransformer - Class in net.sf.basedb.util.listable

Source item transformer implementation that transform raw bioassay items to derived bioassays.

RawBioAssayToDerivedBioAssayTransformer() - Constructor for class net.sf.basedb.util.listable.RawBioAssayToDerivedBioAssayTransformer

Create a new raw bioassay to derived bioassay transformer.

RawBioAssayValidator - Class in net.sf.basedb.util.overview.validator

Validator implementation for raw bioassays and root raw bioassays.

RawBioAssayValidator() - Constructor for class net.sf.basedb.util.overview.validator.RawBioAssayValidator

RawChannelFunction - Class in net.sf.basedb.util.jep

A JEP function class that adds a rawCh(int) function to a JEP expression parser.

RawChannelFunction() - Constructor for class net.sf.basedb.util.jep.RawChannelFunction

Create a new instance of this function.

RawChannelFunction(int[]) - Constructor for class net.sf.basedb.util.jep.RawChannelFunction

Create a new instance of this function which can be used to dynamically evaluate expressions.

rawData - Variable in class net.sf.basedb.util.jep.MeanFunction

rawData - Variable in class net.sf.basedb.util.jep.RawFunction

rawData(String) - Static method in class net.sf.basedb.core.query.Dynamic

Create an expression representing a property of a raw data spot.

rawData(String, String, Type, Formula.AverageMethod, Formatter<?>) - Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory

Create a simple dynamic field that exports a raw data value.

rawData(RawDataProperty, String, Formatter<?>) - Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory

Create a simple dynamic field that exports a raw data value.

RawData - Class in net.sf.basedb.core.data

Represents the measurements for single raw data spot.

RawData() - Constructor for class net.sf.basedb.core.data.RawData

RawData(RawBioAssayData) - Constructor for class net.sf.basedb.core.data.RawData

RAWDATA - Enum constant in enum class net.sf.basedb.core.Item

The item is a RawData spot.

RAWDATA_ID - Static variable in class net.sf.basedb.core.VirtualColumn

This column stores the id of a raw date object.

RAWDATA_INNER - Static variable in class net.sf.basedb.core.DynamicSpotQueryJoiners

This instance joins raw data with an inner join.

RAWDATA_LEFT - Static variable in class net.sf.basedb.core.DynamicSpotQueryJoiners

This instance joins raw data with a left join.

rawDataBatcher - Variable in class net.sf.basedb.core.RawBioAssay

RawDataBatcher - Class in net.sf.basedb.core

Batcher class for raw data.

RawDataBatcher(DbControl, RawBioAssay, FeatureIdentificationMethod) - Constructor for class net.sf.basedb.core.RawDataBatcher

RawDataBatcher.FeatureInfo - Class in net.sf.basedb.core

RawDataBatcher.FeatureProxy - Class in net.sf.basedb.core

RawDataBatcher.ReporterProxy - Class in net.sf.basedb.core

RawDataFlatFileImporter - Class in net.sf.basedb.plugins

A plugin that imports rawdata from a flatfile.

RawDataFlatFileImporter() - Constructor for class net.sf.basedb.plugins.RawDataFlatFileImporter

RawDataFlatFileImporter.FileIterator - Class in net.sf.basedb.plugins

RawDataJoiner(JoinType) - Constructor for class net.sf.basedb.core.DynamicSpotQueryJoiners.RawDataJoiner

rawDataMember - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

RawDataProperty - Class in net.sf.basedb.core

Holds information about an extended property for raw data.

RawDataProperty(String, String, String, String, Type, int, boolean, Formula.AverageMethod, int) - Constructor for class net.sf.basedb.core.RawDataProperty

Create a new rawdata property.

RawDataPropertyExpression - Class in net.sf.basedb.core

An expression representing the property of a raw data spot.

RawDataPropertyExpression(String) - Constructor for class net.sf.basedb.core.RawDataPropertyExpression

RawDataProxy() - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileImporter.RawDataProxy

rawDataType - Variable in class net.sf.basedb.core.data.ExperimentData

rawDataType - Variable in class net.sf.basedb.core.data.FormulaData

rawDataType - Variable in class net.sf.basedb.core.data.ItemListData

rawDataType - Variable in class net.sf.basedb.core.data.PlatformData

rawDataType - Variable in class net.sf.basedb.core.data.PlatformVariantData

rawDataType - Variable in class net.sf.basedb.core.data.RawBioAssayData

rawDataType - Variable in class net.sf.basedb.core.DynamicRawDataQuery

rawDataType - Variable in class net.sf.basedb.core.MigrateRbaToDba.Itemlist

rawDataType - Variable in class net.sf.basedb.core.MigrateRbaToDba.LineMapping

rawDataType - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba

rawDataType - Variable in class net.sf.basedb.core.RawDataBatcher

The type of raw data to batch.

rawDataType - Variable in class net.sf.basedb.util.jep.RawFunction

RawDataType - Class in net.sf.basedb.core

This class holds information about a raw data type.

RawDataType(String, String, String, int, boolean, PlatformData, PlatformVariantData, String, List<RawDataProperty>, List<IntensityFormula>) - Constructor for class net.sf.basedb.core.RawDataType

RawDataType(String, String, String, int, String, List<RawDataProperty>, List<IntensityFormula>) - Constructor for class net.sf.basedb.core.RawDataType

Create a new RawDataType.

RawDataType(PlatformData) - Constructor for class net.sf.basedb.core.RawDataType

Create a new raw data type representing a file-only platform.

RawDataType(PlatformVariantData) - Constructor for class net.sf.basedb.core.RawDataType

Create a new raw data type representing a file-only platform variant.

rawDataTypeColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

RawDataTypeFilter - Class in net.sf.basedb.clients.web.extensions.list

Filter implementation that accept raw bioassay items of a given raw data type.

RawDataTypeFilter(RawDataType) - Constructor for class net.sf.basedb.clients.web.extensions.list.RawDataTypeFilter

rawDataTypeMapper - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

rawDataTypeParameter - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

rawDataTypes - Static variable in class net.sf.basedb.core.RawDataTypes

A map from raw data type name --> RawDataType.

RawDataTypes - Class in net.sf.basedb.core

This class is used for reading the XML configuration file with information about raw data types.

RawDataTypes() - Constructor for class net.sf.basedb.core.RawDataTypes

RawDataTypes.NameComparator - Class in net.sf.basedb.core

Comparator implementation that sorts raw data types according to their name.

rawDataTypesFile - Static variable in class net.sf.basedb.core.Application

The path to the file containing raw data types.

rawDataTypeType - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

RawDataUtil - Class in net.sf.basedb.core

Utiltity class for getting and setting non-public properties of raw data objects.

RawDataUtil() - Constructor for class net.sf.basedb.core.RawDataUtil

rawField(String, String, Type, Formula.AverageMethod) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin

rawField(String, String, Type, Formula.AverageMethod) - Method in class net.sf.basedb.plugins.BfsExporterPlugin

RawFunction - Class in net.sf.basedb.util.jep

A JEP function class that adds a raw(string) function to a JEP expression parser.

RawFunction(boolean) - Constructor for class net.sf.basedb.util.jep.RawFunction

Create a new instance of this function.

RawFunction(DbControl, RawDataType, boolean) - Constructor for class net.sf.basedb.util.jep.RawFunction

Create a new instance of this function working with raw data of the specified raw data type.

RawMappingQuery(DataCube) - Constructor for class net.sf.basedb.core.DataCube.RawMappingQuery

rawMappingSql - Variable in class net.sf.basedb.core.MappingBatcher

The statement that inserts the spot/raw data link.

rawMappingSqlStatement - Variable in class net.sf.basedb.core.MappingBatcher

The SQL string for the MappingBatcher.rawMappingSql statement.

rawParents - Variable in class net.sf.basedb.core.data.BioAssayData

RAWPARENTS - Enum constant in enum class net.sf.basedb.core.VirtualTable

Table that maps column/position coordinates in a data cube to the id's of the raw spots their intensities where calculated from.

rawSources - Variable in class net.sf.basedb.core.data.TransformationData

rba - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter.BatchAndMapHolder

rba - Variable in class net.sf.basedb.util.affymetrix.CelValidationAction

Rba(Object[]) - Constructor for class net.sf.basedb.core.MigrateRbaToDba.Rba

rbaId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba

rdt - Variable in class net.sf.basedb.clients.web.extensions.list.RawDataTypeFilter

read - Static variable in class net.sf.basedb.core.Item.DefinedPermissions

read() - Method in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream

read() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.WorkbookStream

read() - Method in class net.sf.basedb.util.gtf.GtfInputStream

read() - Method in class net.sf.basedb.util.InputStreamCombiner

read() - Method in class net.sf.basedb.util.InputStreamSplitter

read() - Method in class net.sf.basedb.util.InputStreamTracker

read(byte[]) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream

read(byte[]) - Method in class net.sf.basedb.core.Migration.ProgressInputStream

read(byte[]) - Method in class net.sf.basedb.util.gtf.GtfInputStream

read(byte[]) - Method in class net.sf.basedb.util.InputStreamCombiner

read(byte[]) - Method in class net.sf.basedb.util.InputStreamSplitter

read(byte[]) - Method in class net.sf.basedb.util.InputStreamTracker

read(byte[], int, int) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream

read(byte[], int, int) - Method in class net.sf.basedb.core.Migration.ProgressInputStream

read(byte[], int, int) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.WorkbookStream

read(byte[], int, int) - Method in class net.sf.basedb.util.gtf.GtfInputStream

read(byte[], int, int) - Method in class net.sf.basedb.util.InputStreamCombiner

read(byte[], int, int) - Method in class net.sf.basedb.util.InputStreamSplitter

read(byte[], int, int) - Method in class net.sf.basedb.util.InputStreamTracker

read(byte[], int, int) - Method in class net.sf.basedb.util.ProgressInputStream

read(InputStream) - Static method in class net.sf.basedb.util.FileUtil

Read from the input stream until the end is reached.

read(String, int) - Method in class net.sf.basedb.util.StaticCache

Get an input stream for reading binary information from the cache.

read(String, OutputStream, int) - Method in class net.sf.basedb.util.StaticCache

Read binary information from the cache.

read(Socket, boolean) - Static method in class net.sf.basedb.util.SocketUtil

Read input from a socket.

READ - Enum constant in enum class net.sf.basedb.core.Permission

This permission allows a user read information about an item.

readData(DbControl, DynamicSpotQuery, BioAssay, MACalculator) - Method in class net.sf.basedb.plugins.LowessNormalization

reader - Variable in class net.sf.basedb.util.gtf.GtfInputStream

reader - Variable in class net.sf.basedb.util.parser.FlatFileParser

Reads from the given input stream

readFormData(byte[]) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload

Read from ServletInputStream until the boundary is found.

readLine(byte[], int, int) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload

Read next line of data into a buffer.

readLineAsString() - Method in class net.sf.basedb.clients.web.fileupload.FileUpload

Reads the next line of input and returns it as a string.

readLock - Variable in class net.sf.basedb.util.StaticCache.State

readLock() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile

Try to aquire a read-lock.

readLock() - Method in class net.sf.basedb.util.StaticCache.LockEntry

readMore() - Method in class net.sf.basedb.util.gtf.GtfInputStream

Read more data from the GTF file.

readMoreData() - Method in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream

Read the next line from the ServletInputStream until the boundary is found on a line by itself.

readObject(ObjectInputStream) - Method in class net.sf.basedb.clients.web.taglib.extensions.Render

readObject(ObjectInputStream) - Method in class net.sf.basedb.clients.web.taglib.extensions.Scripts

readObject(ObjectInputStream) - Method in class net.sf.basedb.clients.web.taglib.extensions.Stylesheets

readObject(ObjectInputStream) - Method in class net.sf.basedb.clients.web.taglib.table.ExtensionCells

readObject(ObjectInputStream) - Method in class net.sf.basedb.core.data.ContextIndex

readObject(ObjectInputStream) - Method in class net.sf.basedb.core.data.FileTypeIndex

readObject(ObjectInputStream) - Method in class net.sf.basedb.core.data.QuotaIndex

readObject(ObjectInputStream) - Method in class net.sf.basedb.core.data.ReporterListScoreData

readObject(ObjectInputStream) - Method in class net.sf.basedb.core.log.LoggingInterceptor

readObject(ObjectInputStream) - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot

readObject(ObjectInputStream) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

readObject(ObjectInputStream) - Method in class net.sf.basedb.util.jep.FunctionSafeJep.SafeFunctionTable

readPermissions - Variable in class net.sf.basedb.core.Job.SignalKeyring

readSectionHeaders() - Method in class net.sf.basedb.clients.web.fileupload.FileUpload

Read from ServletInputStream until an empty line is found.

readToBoundary(byte[]) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload

Read from ServletInputStream until the boundary is found on a line by itself.

readToEnd - Variable in class net.sf.basedb.util.InputStreamSplitter

If the remainder of the input stream should be copied if it is closed before the end.

readValue(ObjectInputStream) - Method in enum class net.sf.basedb.core.Type

Read a value of this type to the input stream.

readWorkbook(InputStream) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil

Read an Excel workbook from the stream.

RealJoin - Class in net.sf.basedb.core

Represents a join from one virtual table in the dynamic database to a table in the regular database or between two tables in the regular database.

RealJoin(JoinType, RealTable, RealTable, String) - Constructor for class net.sf.basedb.core.RealJoin

Create a new join between two regular tables.

RealJoin(JoinType, VirtualTable, RealTable, VirtualColumn) - Constructor for class net.sf.basedb.core.RealJoin

Create a new join between a virtual and a regular table.

realTable - Variable in class net.sf.basedb.core.RawDataType

RealTable - Class in net.sf.basedb.core

This class defines constants that are used to specify a table in the regular (non-dynamic) database while doing analysis with dynamic queries.

RealTable(String, String) - Constructor for class net.sf.basedb.core.RealTable

Creates a new table.

reattachItem(T, boolean) - Method in class net.sf.basedb.core.DbControl

Reattach a detached item from this DbControl.

recalculateFreeWells(ProgressReporter) - Static method in class net.sf.basedb.core.Update

Vefify and update the free wells of all bioplates.

recalculateRemainingQuantity(ProgressReporter) - Static method in class net.sf.basedb.core.Update

Vefify and update the remaining quantity of all biomaterials.

received - Variable in class net.sf.basedb.core.signal.DelegatingSignalHandler

List holding received signals.

received - Variable in class net.sf.basedb.core.signal.EnhancedThreadSignalHandler

received - Variable in class net.sf.basedb.core.signal.ProgressReporterSignalHandler

receiverId - Variable in class net.sf.basedb.core.signal.AbstractSignalReceiver

receiverId - Variable in class net.sf.basedb.core.signal.LocalSignalReceiver

receivers - Static variable in class net.sf.basedb.core.signal.LocalSignalReceiver

Holds all registered signal receivers.

recent - Variable in class net.sf.basedb.clients.web.taglib.Select

List of recently used items.

reconnect() - Method in class net.sf.basedb.core.DbControl

Deprecated.

In 3.12. Applications should use separate DbControl instead.

reconnect(Connection) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

recursive - Variable in class net.sf.basedb.util.OlderThanFileFilter

recycle(DbControl, Annotatable) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper

Re-cycle transactions if needed and re-load the given item in the new transaction.

redefinedColumnNames - Variable in class net.sf.basedb.util.basefile.BaseFileParser

REF_SEQ_GTF - Static variable in class net.sf.basedb.core.DataFileType

The external ID for the file type representing a GTF reference file that define the features on an array design that we are interested in.

refColumns - Variable in class net.sf.basedb.core.dbengine.TableInfo.ForeignKeyInfo

referenceFactor - Variable in class net.sf.basedb.core.data.UnitData

referenceNotFoundErrorParameter - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

referenceOffset - Variable in class net.sf.basedb.core.data.UnitData

referenceUnit - Variable in class net.sf.basedb.core.data.QuantityData

ReflectValidationRuleActionFactory - Class in net.sf.basedb.util.overview.extensions

Factory implementation for validation rule actions that uses reflection to access the value of a public static field and return that as the validation rule.

ReflectValidationRuleActionFactory() - Constructor for class net.sf.basedb.util.overview.extensions.ReflectValidationRuleActionFactory

refName - Variable in class net.sf.basedb.core.dbengine.TableInfo.ForeignKeyInfo

refresh(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

refresh(Object) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

refresh(Object, Map<String, Object>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

refresh(Object, LockModeType) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

refresh(Object, LockModeType, Map<String, Object>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

refresh(Object, LockMode) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

refresh(Object, LockMode) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

refresh(Object, LockOptions) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

refresh(String, Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

refresh(String, Object) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

refresh(String, Object, LockMode) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

refresh(String, Object, LockOptions) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

refresh(Session, BasicData) - Static method in class net.sf.basedb.core.HibernateUtil

Reload the data from the database for a given entity.

refreshItem(BasicItem) - Method in class net.sf.basedb.core.DbControl

Reload the item from the database.

regexp - Variable in class net.sf.basedb.core.ExtendedPropertyLinker

regexp - Variable in class net.sf.basedb.core.query.RlikeRestriction

RegexpFileFilter - Class in net.sf.basedb.util

An implementation of the FileFilter interface that filter files and directories based on regular expressions.

RegexpFileFilter(String, String) - Constructor for class net.sf.basedb.util.RegexpFileFilter

Create a new file filter from a string regular expressions.

RegexpFileFilter(Pattern, Pattern) - Constructor for class net.sf.basedb.util.RegexpFileFilter

Create a new file filter from patterns.

region - Variable in class net.sf.basedb.util.GeoLocation

register(Registry, String, String) - Static method in class net.sf.basedb.clients.web.extensions.list.ListColumnUtil

register(Registry, String, String) - Static method in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil

registerAgent() - Method in class net.sf.basedb.clients.jobagent.AgentController

registerCheckedNodeLoader(Object, Class<? extends NodeLoader<? extends BasicItem>>) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory

Register a node loader implementation that you are sure fulfills the requirements.

registerCheckedNodeValidator(Object, Class<?>) - Method in class net.sf.basedb.util.overview.validator.BasicItemNodeValidatorFactory

Register a node loader implementation that you are sure fulfills the requirements.

registerCleanup(Object, Runnable) - Static method in class net.sf.basedb.core.Application

Register an action that needs to be performed when the monitored object becomes unreachable.

registerConverter(Object, JepConversionFunction<?>) - Static method in class net.sf.basedb.util.jep.convert.ConverterFactory

Add a converter for a specific object.

registerCustomRequestHandlers(MultiProtocolRequestHandler) - Method in class net.sf.basedb.clients.jobagent.Agent

registerDefaultNodeLoaders() - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory

Registers default item node loaders from BioSource to Experiment, etc.

registerDefaultNodeValidators() - Method in class net.sf.basedb.util.overview.validator.BasicItemNodeValidatorFactory

Registers default item node validators from BioSource to Experiment, etc.

registerDelayedFilters(Metadata) - Method in class net.sf.basedb.core.HibernateUtil.FilterConfigurator

Register all filters that has been stored by HibernateUtil.FilterConfigurator.createItemSpecificFilter(String, Item, String, Element)

Registered - Interface in net.sf.basedb.core

Items that implements this interface has their registration date stored in the database.

RegisteredAbout(About) - Constructor for class net.sf.basedb.util.extensions.Registry.RegisteredAbout

Create a new registered about by copying the information from the parameter.

registeredColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Column mapping parameter for the item registration date.

RegisteredData - Interface in net.sf.basedb.core.data

Adds the date an item was registered in the database.

RegisteredEventHandler(EventHandler, EventFilter, ClassLoader) - Constructor for class net.sf.basedb.util.extensions.Registry.RegisteredEventHandler

RegisteredExtension(Extension<A>, Registry.RegisteredExtensionPoint<? super A>, ClassLoader) - Constructor for class net.sf.basedb.util.extensions.Registry.RegisteredExtension

Create a new registered extension by copying the information from the parameter.

RegisteredExtensionPoint(ExtensionPoint<A>, ClassLoader) - Constructor for class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint

Create a new registered extension point by copying the information from the parameter.

registerEditTab(Registry, String, String) - Static method in class net.sf.basedb.clients.web.extensions.edit.EditUtil

registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter

registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter

registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.ArraySlideImporter

registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter

registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.BioSourceImporter

registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter

registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.KitImporter

registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter

registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter

registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.TagImporter

registerEventHandler(EventHandler, EventFilter, ClassLoader) - Method in class net.sf.basedb.util.extensions.Registry

Register an event handler for responding to events happening to extension points and extensions in the registry.

registerExtension(Extension<A>, ClassLoader) - Method in class net.sf.basedb.util.extensions.Registry

Register an extension.

registerExtensionPoint(ExtensionPoint<A>, ClassLoader) - Method in class net.sf.basedb.util.extensions.Registry

Register an extension point.

registerExtensionPoints(RegisterExtensionsProcessor.FileData, Registry, boolean) - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor

registerExtensionPoints(Registry) - Static method in class net.sf.basedb.clients.web.extensions.edit.EditUtil

Registers tabcontrol and on-save extension points with the given registry.

registerExtensionPoints(Registry) - Static method in class net.sf.basedb.clients.web.extensions.list.ListColumnUtil

registerExtensionPoints(Registry) - Static method in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil

registerExtensionPoints(Registry, boolean) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader

Register all loaded extension points with a registry.

registerExtensions(RegisterExtensionsProcessor.FileData, ExtensionsManager, boolean) - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor

registerExtensions(Registry, boolean) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader

Register all loaded extensions with a registry.

RegisterExtensionsProcessor - Class in net.sf.basedb.util.extensions.manager.processor

Extension file processor implementation that will load the extension definitions from each file and register them with the registry that is managed by the manager.

RegisterExtensionsProcessor(XmlLoader, ProcessResults) - Constructor for class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor

Create a new processor.

RegisterExtensionsProcessor.FileData - Class in net.sf.basedb.util.extensions.manager.processor

Keep track of the extension points and extensions found in a file.

registerFactory(RegisterExtensionsProcessor.FileData, Object) - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor

Register factory parameters for the given factory instance.

registerFileOnlyRawDataType(RawDataType) - Static method in class net.sf.basedb.core.RawDataTypes

registerFormatter(Class<? extends T>, Formatter<T>) - Method in class net.sf.basedb.util.formatter.MultiFormatter

Register a formatter for the specified class.

registerHandler(RequestHandler, String...) - Method in class net.sf.basedb.clients.jobagent.handlers.DefaultRequestHandler

registerMetadata(ObjectKey<M>, M) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile

Register metadata about an object.

registerNodeLoader(Object, Class<? extends NodeLoader<? extends BasicItem>>) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory

Register a node loader implementation.

registerNodeValidator(Item, Class<? extends NodeValidator<? extends BasicItem>>) - Method in class net.sf.basedb.util.overview.validator.BasicItemNodeValidatorFactory

Register a node validator implementation.

registerObject(ObjectKey<?>, ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager

Register an object as defined by the given extensions file.

registerObject(ObjectKey<O>, O) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile

Register an object as "defined" by this extensions file.

registerOnSave(Registry, String, String, RethrowErrorHandlerFactory) - Static method in class net.sf.basedb.clients.web.extensions.edit.EditUtil

registerParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.core.PluginRequest

Keep track of all parameters so that we can save label and description in the ParameterValuesImpl.saveParameters(Job, Map) method.

registerProtocols(RequestHandler, String...) - Method in class net.sf.basedb.clients.jobagent.handlers.MultiProtocolRequestHandler

Register a handler for one or more protocols.

registerRequestHandler(RequestHandler, String...) - Method in class net.sf.basedb.clients.jobagent.Agent

Register a request handler for one or more protocols.

registerSignal(String, String, String) - Static method in class net.sf.basedb.core.signal.Signal

Register a signal.

registerSignalHandler(SignalHandler) - Method in class net.sf.basedb.clients.web.util.SimpleSignalProgressReporter

This return null when there is no need for a global id.

registerSignalHandler(SignalHandler) - Method in class net.sf.basedb.core.signal.AbstractSignalReceiver

Register a signal handler with this receiver.

registerSignalHandler(SignalHandler) - Method in class net.sf.basedb.core.signal.DelegatingSignalHandler

Register a signal handler to delegate to.

registerSignalHandler(SignalHandler) - Method in interface net.sf.basedb.core.signal.SignalReceiver

Register a signal handler with this receiver.

registerSignalReceiver(SignalReceiver) - Method in class net.sf.basedb.core.PluginExecutionRequest

Register a signal receiver that will receive signals for this job.

registry - Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl

registry - Variable in class net.sf.basedb.util.extensions.ExtensionPointContext

registry - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsManager

Registry - Class in net.sf.basedb.util.extensions

A registry for keeping track of extensions points and installed extensions.

Registry() - Constructor for class net.sf.basedb.util.extensions.Registry

Create a new empty registry.

Registry.AttributeKey - Class in net.sf.basedb.util.extensions

Identifies attribute.

Registry.RegisteredAbout - Class in net.sf.basedb.util.extensions

Registry.RegisteredEventHandler - Class in net.sf.basedb.util.extensions

Registry.RegisteredExtension<A extends Action> - Class in net.sf.basedb.util.extensions

Internal representation of an extension.

Registry.RegisteredExtensionPoint<A extends Action> - Class in net.sf.basedb.util.extensions

Internal representation of an extension point.

registryBuilder - Variable in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration

relatedAnnotationTypes - Variable in class net.sf.basedb.core.ItemSubtype

RelatedItemAnnotationColumn - Class in net.sf.basedb.clients.web.extensions.list

Related item column that load annotation values from the parent or child items.

RelatedItemAnnotationColumn(DbControl, int, RelatedItemColumn.Specification, RelatedItemHelper, AnnotationType) - Constructor for class net.sf.basedb.clients.web.extensions.list.RelatedItemAnnotationColumn

RelatedItemColumn - Class in net.sf.basedb.clients.web.extensions.list

A column action implementation that finds a parent or child item of a given subtype and then get an annotation or other property value from it.

RelatedItemColumn(DbControl, int, RelatedItemColumn.Specification, RelatedItemHelper) - Constructor for class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn

RelatedItemColumn.Specification - Class in net.sf.basedb.clients.web.extensions.list

Represents a specification for loading a related parent or child item.

RelatedItemColumnActionFactory - Class in net.sf.basedb.clients.web.extensions.list

Action factory for adding columns to a table that pull data from a parent or child item from an arbitrary location up or down the chain of linked items.

RelatedItemColumnActionFactory() - Constructor for class net.sf.basedb.clients.web.extensions.list.RelatedItemColumnActionFactory

RelatedItemErrorColumn - Class in net.sf.basedb.clients.web.extensions.list

Related item column that displays an error message.

RelatedItemErrorColumn(int, RelatedItemColumn.Specification, RelatedItemHelper, String) - Constructor for class net.sf.basedb.clients.web.extensions.list.RelatedItemErrorColumn

RelatedItemExtensionColumn - Class in net.sf.basedb.clients.web.extensions.list

Related item column that get values from an extension.

RelatedItemExtensionColumn(DbControl, int, RelatedItemColumn.Specification, RelatedItemHelper, ListColumnAction<Annotatable, ?>) - Constructor for class net.sf.basedb.clients.web.extensions.list.RelatedItemExtensionColumn

RelatedItemHelper - Class in net.sf.basedb.clients.web.extensions.list

Helper class for storing request-scoped objects that may be useful to re-use between multiple columns.

RelatedItemHelper(SessionControl, JspContext, boolean) - Constructor for class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper

RelatedItemHelper.CloseMyDbControl - Class in net.sf.basedb.clients.web.extensions.list

RelatedItemListColumn - Class in net.sf.basedb.clients.web.extensions.list

Related item column that get the item lists that the parent or child item is a member of.

RelatedItemListColumn(DbControl, int, RelatedItemColumn.Specification, Filter<? super ItemList>, RelatedItemHelper) - Constructor for class net.sf.basedb.clients.web.extensions.list.RelatedItemListColumn

RelatedItemMultiHopColumn - Class in net.sf.basedb.clients.web.extensions.list

Related item column that get values from multiple hops betweeen child->parent->child.

RelatedItemMultiHopColumn(DbControl, int, RelatedItemColumn.Specification, RelatedItemHelper, RelatedItemColumn) - Constructor for class net.sf.basedb.clients.web.extensions.list.RelatedItemMultiHopColumn

RelatedItemPropertyColumn - Class in net.sf.basedb.clients.web.extensions.list

Related item column that get values from parent or child items by specifying a "property path".

RelatedItemPropertyColumn(DbControl, int, RelatedItemColumn.Specification, RelatedItemHelper, Metadata.PropertyPath<? super Annotatable, ?>) - Constructor for class net.sf.basedb.clients.web.extensions.list.RelatedItemPropertyColumn

relatedItems - Static variable in class net.sf.basedb.core.ItemSubtype

relatedSubtypes - Variable in class net.sf.basedb.core.data.ItemSubtypeData

release() - Method in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget

releaseRemoteSlot(String) - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager

Release the remote slot with the given id.

releaseSavepoint(Connection, Savepoint, String) - Method in class net.sf.basedb.core.AbstractSqlQuery

Release the given savepoint.

releaseSlot(Slot) - Method in class net.sf.basedb.clients.jobagent.slotmanager.InternalSlotManager

releaseSlot(Slot) - Method in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager

releaseSlot(Slot) - Method in interface net.sf.basedb.clients.jobagent.slotmanager.SlotManager

Called by the job agent when the job has finished exeuting.

reload - Variable in class net.sf.basedb.core.Keyring

TRUE if the Timer has signaled that it is time to reload the information.

reload() - Method in class net.sf.basedb.core.Keyring

Reload all permission information

reloadPermissions() - Method in class net.sf.basedb.core.SessionControl

Tell the core to reload the logged in users permission the next time the client application needs to check the permissions.

reloadSettings(boolean, boolean) - Method in class net.sf.basedb.core.SessionControl

Reloads user- and client-specific settings.

ReloadTask() - Constructor for class net.sf.basedb.core.Keyring.ReloadTask

remainingQuantity - Variable in class net.sf.basedb.core.data.MeasuredBioMaterialData

RemainingQuantityAction(DbControl, MeasuredBioMaterialData) - Constructor for class net.sf.basedb.core.MeasuredBioMaterial.RemainingQuantityAction

remapAllTo(ImageRemapper, String) - Static method in class net.sf.basedb.clients.web.extensions.skin.ImageRemapperUtil

Scan the given url for images (png and gif) and remap them.

remapDir - Variable in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory

remapImages(ImageRemapper) - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory.MySkinAction

remapImages(ImageRemapper) - Method in interface net.sf.basedb.clients.web.extensions.skin.SkinAction

Remap images to another location.

remember - Variable in class net.sf.basedb.clients.web.taglib.tab.TabControl

If it should try to remember the last active tab on the page

rememberLast - Variable in class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory

rememberLastLogin - Variable in class net.sf.basedb.clients.web.extensions.login.LoginFormBean

rememberLastLogin() - Method in interface net.sf.basedb.clients.web.extensions.login.LoginFormAction

If TRUE, the browser is asked to remember the last login used.

rememberLastLogin() - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean

rememberLastLogin() - Method in class net.sf.basedb.clients.web.extensions.login.PasswordLoginFormFactory

remote - Variable in class net.sf.basedb.clients.jobagent.Agent

remoteHost - Variable in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager

remoteId - Variable in class net.sf.basedb.core.data.SessionData

remoteId - Variable in class net.sf.basedb.core.data.UserDeviceData

remoteId - Variable in class net.sf.basedb.core.SessionControl

The remote IP.

remotePort - Variable in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager

remoteRequestHandler - Variable in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager

RemoteSlot(Slot) - Constructor for class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlot

RemoteSlotManager - Class in net.sf.basedb.clients.jobagent.slotmanager

Slot manager implementation that requests slots from another job agent.

RemoteSlotManager() - Constructor for class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager

RemoteSlotManager.RemoteSlotPinger - Class in net.sf.basedb.clients.jobagent.slotmanager

Task that is scheduled at regular intervals to send ping commands to the remote host.

RemoteSlotPinger(RemoteSlotManager) - Constructor for class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager.RemoteSlotPinger

RemoteSlotRequestHandler(MasterSlotManager) - Constructor for class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlotRequestHandler

remoteSlots - Variable in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager

remoteSlots - Variable in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager

RemoteSlotTimeoutChecker(MasterSlotManager) - Constructor for class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlotTimeoutChecker

Removable - Interface in net.sf.basedb.core

A Removable item is an item that can be flagged as removed.

REMOVABLE_FILTER - Static variable in class net.sf.basedb.core.QueryRuntimeFilterFactory

RemovableData - Interface in net.sf.basedb.core.data

A removable item is an item that can be flagged as removed.

RemovableFilter() - Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.RemovableFilter

removableItems - Static variable in class net.sf.basedb.core.Metadata

RemovableUtil - Class in net.sf.basedb.util

RemovableUtil() - Constructor for class net.sf.basedb.util.RemovableUtil

remove - Variable in class net.sf.basedb.util.annotations.InheritSpecification

remove() - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator

Not supported.

remove() - Method in class net.sf.basedb.core.DataResultIterator

Not supported.

remove() - Method in class net.sf.basedb.core.DynamicResultIterator

Not supported.

remove() - Method in class net.sf.basedb.core.ItemResultIterator

Not supported.

remove() - Method in class net.sf.basedb.core.ItemResultList.ResultListIterator

This operation is not supported.

remove() - Method in class net.sf.basedb.core.ItemResultList.ResultListListIterator

This operation is not supported.

remove() - Method in class net.sf.basedb.core.ReporterScoreResultIterator

Not supported.

remove() - Method in class net.sf.basedb.core.ScrollIterator

Not supported.

remove() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter.FileIterator

remove() - Method in class net.sf.basedb.util.ArrayIterator

This operation is not supported.

remove() - Method in class net.sf.basedb.util.extensions.ActionIterator

Not supported.

remove() - Method in class net.sf.basedb.util.NestedIterator

This operation is not supported.

remove() - Method in class net.sf.basedb.util.query.MultiQueryIterator

remove() - Method in class net.sf.basedb.util.Tree.ElementIterator

Not supported.

remove() - Method in class net.sf.basedb.util.Tree.EntryIterator

Not supported.

remove(int) - Method in class net.sf.basedb.core.AbstractResultList

Not supported.

remove(int) - Method in class net.sf.basedb.core.UnmodifiableResultList

Not supported.

remove(int) - Method in class net.sf.basedb.util.Enumeration

remove(Object) - Method in class net.sf.basedb.core.AbstractResultList

Not supported.

remove(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

remove(Object) - Method in class net.sf.basedb.core.UnmodifiableResultList

Not supported.

remove(Object) - Method in class net.sf.basedb.util.formatter.LookupFormatter

Remove an entry from the lookup map.

remove(Object) - Method in class net.sf.basedb.util.Tree

Not supported.

remove(Listable) - Method in class net.sf.basedb.core.ItemList.DelayedAdditionManager

remove(Listable) - Method in class net.sf.basedb.core.ItemList

Deprecated.

In 3.15, use ItemList.removeItem(Listable item) instead

remove(IdListRestriction) - Method in class net.sf.basedb.core.query.IdListRestriction

Merge this id list with another list by removing ids that are found in the other list.

REMOVE - Enum constant in enum class net.sf.basedb.core.log.ChangeType

REMOVE_ONLY - Enum constant in enum class net.sf.basedb.core.ItemList.SynchronizeOption

Synchronize the members by removing items that doesn't match the filter.

removeAll(Collection<?>) - Method in class net.sf.basedb.core.AbstractResultList

Not supported.

removeAll(Collection<?>) - Method in class net.sf.basedb.core.UnmodifiableResultList

Not supported.

removeAll(Collection<?>) - Method in class net.sf.basedb.util.Tree

Not supported.

removeAll(ItemList) - Method in class net.sf.basedb.core.ItemList

Remove all items from this list that are present in the other list.

removeAll(ItemList.DelayedAdditionManager) - Method in class net.sf.basedb.core.ItemList.DelayedAdditionManager

removeAll(ReporterList) - Method in class net.sf.basedb.core.ReporterList

Remove all reporters from this list that are present in the other list.

removeAllInherited(AnnotationSet) - Method in class net.sf.basedb.core.AnnotationSet

Utility method to stop inheriting all annotations in the given annotation set.

removeAllMembers() - Method in class net.sf.basedb.core.FileSet

Remove all members in a file set.

removeAllOfType(DataFileType) - Method in class net.sf.basedb.core.FileSet

Remove all member files of the given type.

removeAllOfTypeExcept(DataFileType, File) - Method in class net.sf.basedb.core.FileSet

Remove all member files of the given type.

removeAllPropertyFilters() - Method in class net.sf.basedb.core.ItemContext

Remove all property filters from this context.

removeAllPropertyFilters(String) - Method in class net.sf.basedb.core.ItemContext

Remove all property filters for the given property.

removeAllTemporaryFilters() - Method in class net.sf.basedb.core.ItemContext

Remove all temporary filters.

RemoveAllTransformer<I> - Class in net.sf.basedb.util.collections

Collection transformer implementation that removes all elements in the source collection from the destination collection.

RemoveAllTransformer() - Constructor for class net.sf.basedb.util.collections.RemoveAllTransformer

removeAnnotation(AnnotationType) - Method in class net.sf.basedb.core.AnnotationSet

Delete the primary annotation of the specified annotation type.

removeAnnotations() - Method in interface net.sf.basedb.core.Annotatable

Remove all annotations from this item, by deleting the annotation set.

removeAnnotations() - Method in class net.sf.basedb.core.AnnotatedItem

removeAnnotations() - Method in class net.sf.basedb.core.BioAssay

removeAnnotations() - Method in class net.sf.basedb.core.BioAssaySet

removeAnnotations() - Method in class net.sf.basedb.core.PluginDefinition

removeAnnotations() - Method in class net.sf.basedb.core.Project

removeAnnotations() - Method in class net.sf.basedb.core.RootRawBioAssay

removeAnnotations() - Method in class net.sf.basedb.core.Well

removeAnyToAnyLinkedTo(DbControl, ItemQuery<AnyToAny>, boolean) - Static method in class net.sf.basedb.util.RemovableUtil

removeAssociatedDataFileType(DataFileType) - Method in class net.sf.basedb.core.ItemSubtype

Remove the association between this subtype and the given data file type.

removeBatcher(Batcher) - Method in class net.sf.basedb.core.DbControl

Remove a Batcher from the batcher queue.

removeCategory(AnnotationTypeCategory) - Method in class net.sf.basedb.core.AnnotationType

Remove a category from this annotation type.

removeClonableProperty(String) - Method in class net.sf.basedb.core.ReporterCloneTemplate

Remove the property with the given name from this template

removeContext(Session, int) - Static method in class net.sf.basedb.core.Update

Remove context-related information for the given item type.

removed - Variable in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter

REMOVED - Enum constant in enum class net.sf.basedb.core.Include

Include items flagged as removed.

removedBy - Variable in class net.sf.basedb.core.data.BioAssaySetData

removedBy - Variable in class net.sf.basedb.core.data.BioPlateEventTypeData

removedBy - Variable in class net.sf.basedb.core.data.BioPlateTypeData

removedBy - Variable in class net.sf.basedb.core.data.CommonData

removedBy - Variable in class net.sf.basedb.core.data.DataFileTypeData

removedBy - Variable in class net.sf.basedb.core.data.ExtraValueTypeData

removedBy - Variable in class net.sf.basedb.core.data.GroupData

removedBy - Variable in class net.sf.basedb.core.data.ItemSubtypeData

removedBy - Variable in class net.sf.basedb.core.data.MessageData

removedBy - Variable in class net.sf.basedb.core.data.MimeTypeData

removedBy - Variable in class net.sf.basedb.core.data.NewsData

removedBy - Variable in class net.sf.basedb.core.data.PlateEventTypeData

removedBy - Variable in class net.sf.basedb.core.data.PlateGeometryData

removedBy - Variable in class net.sf.basedb.core.data.PlatformData

removedBy - Variable in class net.sf.basedb.core.data.PlatformVariantData

removedBy - Variable in class net.sf.basedb.core.data.PluginDefinitionData

removedBy - Variable in class net.sf.basedb.core.data.PluginTypeData

removedBy - Variable in class net.sf.basedb.core.data.ProjectData

removedBy - Variable in class net.sf.basedb.core.data.QuantityData

removedBy - Variable in class net.sf.basedb.core.data.QuotaData

removedBy - Variable in class net.sf.basedb.core.data.ReporterTypeData

removedBy - Variable in class net.sf.basedb.core.data.RoleData

removedBy - Variable in class net.sf.basedb.core.data.TransformationData

removedBy - Variable in class net.sf.basedb.core.data.UnitData

removedBy - Variable in class net.sf.basedb.core.data.UserData

removedBy - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba

removeDefaultItem(BasicItem) - Method in class net.sf.basedb.core.Project

Remove an item from the list of default items for this project.

removeDependingItems(DbControl, Removable, boolean) - Static method in class net.sf.basedb.util.RemovableUtil

Sets the removed-flag for all subitems to a parent

removeEventHandler(EventHandler) - Method in class net.sf.basedb.util.bfs.MultiEventHandler

Removes an event handler.

removeExisting - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

removeExistingParameter - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

removeExperimentalFactor(AnnotationType) - Method in class net.sf.basedb.core.Experiment

Remove an annotation type from the experimental factors for this experiment.

removeExtension(String) - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint

Remove the extension with a given ID.

removeFile(File) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager

Remove a file from the extensions manager.

removeFileSetMembers(DbControl, FileStoreEnabled, boolean) - Static method in class net.sf.basedb.util.RemovableUtil

removeFilesParameter - Variable in class net.sf.basedb.plugins.PackedFileExporter

removeFileType(DataFileType, PlatformVariant) - Method in class net.sf.basedb.core.Platform

Remove a file type from this platform/variant.

removeFilter - Variable in class net.sf.basedb.util.annotations.InheritAnnotationsManager

removeFilterRow(int) - Method in class net.sf.basedb.core.ItemContext

Remove all filters from the specified filter row.

removeFromCache() - Method in class net.sf.basedb.core.MeasuredBioMaterial.RemainingQuantityAction

removeGroup(Group) - Method in class net.sf.basedb.core.Group

Remove a group that is a member of this group.

removeHeader(String) - Method in class net.sf.basedb.core.RawBioAssay

Remove a specific header from the raw bioassay.

removeHeaders() - Method in class net.sf.basedb.core.RawBioAssay

Remove all headers from the raw bioassay.

removeIfPresentIn(int, int, Collection<ItemList>) - Method in class net.sf.basedb.core.ItemList

Remove items that are present in the specified number of lists from this list.

removeIfPresentIn(int, int, Collection<ReporterList>) - Method in class net.sf.basedb.core.ReporterList

Remove reporters that are present in the specified number of lists from this list.

removeIgnore(File) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager

Remove a file from the ignore list.

removeInheritedAnnotation(Annotation) - Method in class net.sf.basedb.core.AnnotationSet

Remove an inherited an annotation.

RemoveInheritedAnnotationsAction(AnnotationType) - Constructor for class net.sf.basedb.core.AnnotationType.RemoveInheritedAnnotationsAction

removeIntersection(Collection<ItemList>) - Method in class net.sf.basedb.core.ItemList

Remove items that are present in ALL OF the given lists from this list.

removeIntersection(Collection<ReporterList>) - Method in class net.sf.basedb.core.ReporterList

Remove reporters that are present in ALL OF the given lists from this list.

removeItem(Listable) - Method in class net.sf.basedb.core.ItemList

Remove an item from the list.

removeItems(Collection<? extends Integer>) - Method in class net.sf.basedb.core.ItemList

Remove all items in the collection from this list.

removeItems(Iterator<? extends Listable>) - Method in class net.sf.basedb.core.ItemList

Remove multiple items from this list in one go.

removeItems(ItemQuery<? extends Listable>) - Method in class net.sf.basedb.core.ItemList

Remove all items that are returned by the query from this list.

removeJobWhenFinished - Variable in class net.sf.basedb.core.data.JobData

removeMember(File, DataFileType) - Method in class net.sf.basedb.core.FileSet

Remove a file as a member from the file set.

removeMember(FileSetMember) - Method in class net.sf.basedb.core.FileSet

Remove the given member from this file set.

removeMembers(Set<Integer>, ItemList.DelayedAdditionManager) - Method in class net.sf.basedb.core.ItemList

Remove members from this list

removeMembersMode - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

removeMode - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

removeObject(String) - Method in class net.sf.basedb.core.ItemContext

Remove a value.

removeParameter(AnnotationType) - Method in class net.sf.basedb.core.Protocol

Remove an annotation type from the parameters for this protocol.

removeParent(DerivedBioAssay) - Method in class net.sf.basedb.core.DerivedBioAssay

Remove a derived bioassay as a parent item for this derived bioassay.

removeParticipant(BioPlate) - Method in class net.sf.basedb.core.BioPlateEvent

Remove the given bioplate from this event.

removePhysicalBioAssay(PhysicalBioAssay) - Method in class net.sf.basedb.core.DerivedBioAssay

Remove a physical bioassay as a parent item for this derived bioassay.

removeProjectAnnotation(AnnotationType, Project) - Method in class net.sf.basedb.core.AnnotationSet

Delete the primary annotation of the specified annotation type.

removePropertyFilter(String) - Method in class net.sf.basedb.core.ItemContext

Remove a property filter on filter row 0.

removePropertyFilter(String, int) - Method in class net.sf.basedb.core.ItemContext

Remove a property filter on the given filter row.

removeRawBioAssay(RawBioAssay) - Method in class net.sf.basedb.core.Experiment

Remove a raw bioassay from this experiment.

removeRecursively(DbControl, Item, Set<Integer>, boolean) - Static method in class net.sf.basedb.util.RemovableUtil

Set the removed flag for selected items, including the subitems.

removeRelatedSubtype(Item) - Method in class net.sf.basedb.core.ItemSubtype

Remove the related subtype for the given item type.

removeReporter(ReporterData) - Method in class net.sf.basedb.core.ReporterList

Remove a reporter from the reporter list.

removeReporters(Set<Integer>) - Method in class net.sf.basedb.core.ReporterList

removeSetting(String) - Method in class net.sf.basedb.core.ItemContext

Remove a value.

removeSignal(Signal) - Method in class net.sf.basedb.core.signal.AbstractSignalHandler

Remove a signal from the list of supported signals.

removeSnapshot(int) - Static method in class net.sf.basedb.core.snapshot.SnapshotManager

Removes a snapshot from the static cache.

removeSnapshots(Collection<Integer>) - Static method in class net.sf.basedb.core.snapshot.SnapshotManager

Removes a list of snapshots from the static cache.

removeSnapshots(List<Integer>) - Static method in class net.sf.basedb.core.snapshot.SnapshotManager

removeSource(BioMaterial) - Method in class net.sf.basedb.core.BioMaterialEvent

Remove a biomaterial used as a source.

removeState() - Method in class net.sf.basedb.core.Job

Remove the saved state from the cache.

removeSymbol(String) - Method in class net.sf.basedb.core.Unit

Remove a symbol from this unit.

removeTemporaryFilter(String) - Method in class net.sf.basedb.core.ItemContext

Remote a temporary filter for the given property on filter row 0.

removeTemporaryFilter(String, int) - Method in class net.sf.basedb.core.ItemContext

Remote a temporary filter for the given property.

removeUnion(Collection<ItemList>) - Method in class net.sf.basedb.core.ItemList

Remove items that are present in at least ONE OF the given lists from this list.

removeUnion(Collection<ReporterList>) - Method in class net.sf.basedb.core.ReporterList

Remove reporters that are present in at least ONE OF the given lists from this list.

removeUsableUnit(Unit) - Method in class net.sf.basedb.core.AnnotationType

Remove a unit from this annotation type.

removeUser(User) - Method in class net.sf.basedb.core.Group

Remove a user that is a member of this group.

removeUser(User) - Method in class net.sf.basedb.core.Role

Revoke this Role from a user.

removeValueConverter(ValueConverter) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader

Remove a converter.

render() - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerUtil

Render the extensions with the current file context information and write it to the JSP output.

render(A) - Method in class net.sf.basedb.clients.web.extensions.renderer.PrefixSuffixRenderer

Deprecated.

render(A) - Method in class net.sf.basedb.util.extensions.AbstractRenderer

Deprecated.

render(A) - Method in interface net.sf.basedb.util.extensions.Renderer

Deprecated.

In 3.19.8, implement the Renderer.render(Action, Extension) method instead. This method will never be called from the BASE core except for the default implementation of Renderer.render(Action, Extension).

render(A, Extension<? extends A>) - Method in class net.sf.basedb.clients.web.extensions.renderer.PrefixSuffixRenderer

render(A, Extension<? extends A>) - Method in interface net.sf.basedb.util.extensions.Renderer

Render the action in the client application.

render(ListColumnAction<I, ?>, Extension<? extends ListColumnAction<I, ?>>) - Method in class net.sf.basedb.clients.web.extensions.list.ListColumnExportRenderer

render(ServiceControllerAction, Extension<? extends ServiceControllerAction>) - Method in class net.sf.basedb.clients.web.extensions.service.StartServiceRenderer

Calls ServiceControllerAction.start() on the service.

render(ServiceControllerAction, Extension<? extends ServiceControllerAction>) - Method in class net.sf.basedb.clients.web.extensions.service.StopServiceRenderer

Calls ServiceControllerAction.stop() on the service.

render(TabAction) - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl

Deprecated.

render(TabAction, Extension<? extends TabAction>) - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl

render(ButtonAction, Extension<? extends ButtonAction>) - Method in class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRenderer

Generates a linked icon:

render(ButtonAction, Extension<? extends ButtonAction>) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarButtonRenderer

Generates a toolbar button.

render(SignalHandler, Extension<? extends SignalHandler>) - Method in class net.sf.basedb.core.signal.ExtensionSignalTransporter.SendSignalRenderer

render(Renderer<A>) - Method in class net.sf.basedb.util.extensions.ExtensionsInvoker

Render all actions using a specific renderer.

render(ValidationAction, Extension<? extends ValidationAction>) - Method in class net.sf.basedb.util.fileset.ResetMetadataRenderer

render(ValidationAction, Extension<? extends ValidationAction>) - Method in class net.sf.basedb.util.fileset.ValidationRenderer

render(Type, List, SessionFactoryImplementor) - Method in class net.sf.basedb.core.hibernate.NativeSQLFunction

Render - Class in net.sf.basedb.clients.web.taglib.extensions

Tag for rendering extensions.

Render() - Constructor for class net.sf.basedb.clients.web.taglib.extensions.Render

renderAsString() - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerUtil

Render the extensions with the current file context information and return it as a string.

renderDefault() - Method in class net.sf.basedb.util.extensions.ExtensionsInvoker

Render all actions using the renderers created by the default renderer factories as specified by the registered extension points and/or extensions.

renderDefault(WrappingRenderer<A>) - Method in class net.sf.basedb.util.extensions.ExtensionsInvoker

Render all actions by wrapping the default renderers by the given wrapping renderer.

renderer - Variable in class net.sf.basedb.clients.web.taglib.extensions.Render

renderer - Variable in class net.sf.basedb.util.extensions.ExtensionContext

renderer - Variable in class net.sf.basedb.util.extensions.ExtensionPointContext

Renderer<A extends Action> - Interface in net.sf.basedb.util.extensions

A renderer is an object that knows how to render an action in the client interface.

rendererFactory - Variable in class net.sf.basedb.util.extensions.ExtensionBean

rendererFactory - Variable in class net.sf.basedb.util.extensions.ExtensionPointBean

rendererFactory - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtension

rendererFactory - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint

RendererFactory<A extends Action> - Interface in net.sf.basedb.util.extensions

A renderer factory is a factory that can create Renderer objects.

renderWithEvent(Renderer<A>, EventType) - Method in class net.sf.basedb.util.extensions.ExtensionsInvoker

Render all actions using a specific renderer and send the specified event to event handlers.

rep - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtension

REPLACE_VALUE - Static variable in class net.sf.basedb.core.ExtendedPropertyLinker

replaceDefaultItem(BasicItem) - Method in class net.sf.basedb.core.Project

Replace an existing default that has the same class and subtype as the given item with the given item.

replaceExisting - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

replaceExisting - Variable in class net.sf.basedb.util.annotations.InheritSpecification

replaceExistingParameter - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

replaceInCommaSeparatedList(String, String, String) - Static method in class net.sf.basedb.core.Update

replacement - Variable in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor

replaceValuesIfDifferent(List<?>, boolean) - Method in class net.sf.basedb.core.data.DateParameterValueData

Overrides the parent method since we need date-specific equals and we want to get rid of the time part of the date.

replaceValuesIfDifferent(List<?>, boolean) - Method in class net.sf.basedb.core.data.ParameterValueData

Replace the values in the database with the new values in the specified list.

replaceValuesIfDifferent(List<?>, boolean) - Method in class net.sf.basedb.core.data.TimestampParameterValueData

Overrides the parent method since we need date-specific equals implementation.

replaceWithJoinAliases(String) - Method in class net.sf.basedb.core.AbstractHqlQuery

Replaces parts of the query with joined aliases.

replicate(Object, ReplicationMode) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

replicate(String, Object, ReplicationMode) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

reporter - Variable in class net.sf.basedb.core.data.FeatureData

reporter - Variable in class net.sf.basedb.core.data.RawData

reporter - Variable in class net.sf.basedb.core.data.ReporterListScoreData

reporter - Variable in class net.sf.basedb.core.data.ReporterTypeData

The reporters that have this type.

reporter - Variable in class net.sf.basedb.core.data.WellData

reporter - Variable in class net.sf.basedb.util.jep.ReporterFunction

reporter(String) - Static method in class net.sf.basedb.core.query.Dynamic

Create an expression representing a property of a reporter.

reporter(String, Boolean) - Static method in class net.sf.basedb.core.query.Dynamic

Create an expression representing a property of a reporter.

reporter(String, String, Type, Formula.AverageMethod, Formatter<?>) - Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory

Create a simple dynamic field that exports reporter annotation values.

reporter(ExtendedProperty, String, Formatter<?>) - Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory

Create a simple dynamic field that exports reporter annotation values.

Reporter - Class in net.sf.basedb.core

This is an utilitiy class for reporters.

Reporter() - Constructor for class net.sf.basedb.core.Reporter

REPORTER - Enum constant in enum class net.sf.basedb.core.Item

The item is a Reporter.

REPORTER - Static variable in class net.sf.basedb.core.File

The id for the FileType item representing a reporter file.

REPORTER_EXTERNAL_ID - Static variable in class net.sf.basedb.core.VirtualColumn

Column for storing the external reporter id.

REPORTER_ID - Static variable in class net.sf.basedb.core.VirtualColumn

This column stores the id of a reporter.

REPORTER_ID_PK - Static variable in class net.sf.basedb.core.VirtualColumn

Column for storing the id of a reporter when it is part of the primary key.

REPORTER_LIST_INNER - Static variable in class net.sf.basedb.core.DynamicPositionQueryJoiners

This instance joins reporter lists with an inner join, unless the ReporterListExpression.getAutoJoinType() method overrides the default.

REPORTER_LIST_INNER - Static variable in class net.sf.basedb.core.DynamicSpotQueryJoiners

This instance joins reporter lists with an inner join, unless the ReporterListExpression.getAutoJoinType() method overrides the default.

REPORTER_LIST_INNER - Static variable in class net.sf.basedb.core.HqlQueryJoiners

This instance joins reporter lists with an inner join, unless the ReporterListExpression.getAutoJoinType() method overrides the default.

REPORTER_LIST_LEFT - Static variable in class net.sf.basedb.core.DynamicPositionQueryJoiners

This instance joins reporter lists with a left join, unless the ReporterListExpression.getAutoJoinType() method overrides the default.

REPORTER_LIST_LEFT - Static variable in class net.sf.basedb.core.DynamicSpotQueryJoiners

This instance joins reporter lists with a left join, unless the ReporterListExpression.getAutoJoinType() method overrides the default.

REPORTER_LIST_LEFT - Static variable in class net.sf.basedb.core.HqlQueryJoiners

This instance joins reporter lists with a left join, unless the ReporterListExpression.getAutoJoinType() method overrides the default.

REPORTER_LIST_SCORES - Static variable in class net.sf.basedb.core.RealTable

REPORTER_MAP - Static variable in class net.sf.basedb.core.File

The id for the FileType item representing a reporter map file.

REPORTER_VERSION - Static variable in class net.sf.basedb.core.VirtualColumn

Column for storing the original version of a reporter that is cloned to a virtual table.

reporterBatcher - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter

reporterBatcher - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

reporterBatcher - Variable in class net.sf.basedb.util.importer.spotdata.PositionEventHandler

ReporterBatcher - Class in net.sf.basedb.core

Batcher class for reporters.

ReporterBatcher(DbControl) - Constructor for class net.sf.basedb.core.ReporterBatcher

reporterCache - Variable in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

reporterCloneBatcher - Variable in class net.sf.basedb.core.Experiment

ReporterCloneBatcher - Class in net.sf.basedb.core

Batcher implementation that is used to handle cloned reporter information in the dynamic database.

ReporterCloneBatcher(DbControl, Experiment) - Constructor for class net.sf.basedb.core.ReporterCloneBatcher

ReporterCloneBatcher.CloneSource - Enum Class in net.sf.basedb.core

Specifies which source table to use for finding out which reporters that are part of the current experiment.

ReporterClonePropertyData - Class in net.sf.basedb.core.data

This class holds information about cloned reporter properties.

ReporterClonePropertyData() - Constructor for class net.sf.basedb.core.data.ReporterClonePropertyData

reporterCloneTemplate - Variable in class net.sf.basedb.core.data.VirtualDbData

ReporterCloneTemplate - Class in net.sf.basedb.core

A reporter clone template is a definition of which reporter properties/annotations that should be cloned to a per-experiment table in the dynamic database.

ReporterCloneTemplate(ReporterCloneTemplateData) - Constructor for class net.sf.basedb.core.ReporterCloneTemplate

REPORTERCLONETEMPLATE - Enum constant in enum class net.sf.basedb.core.Item

The item is a ReporterCloneTemplate.

ReporterCloneTemplateData - Class in net.sf.basedb.core.data

A template for holding information about reporter properties that are/should be cloned in the dynamic database.

ReporterCloneTemplateData() - Constructor for class net.sf.basedb.core.data.ReporterCloneTemplateData

reporterColumnMapping - Static variable in class net.sf.basedb.plugins.PlateFlatFileImporter

ReporterData - Class in net.sf.basedb.core.data

This class represents the idea of clone, oligo or some other reporter for a gene.

ReporterData() - Constructor for class net.sf.basedb.core.data.ReporterData

ReporterData(int) - Constructor for class net.sf.basedb.core.data.ReporterData

Create a reporter object with a given ID.

reporterField - Variable in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField

reporterField - Variable in class net.sf.basedb.plugins.BfsExporterPlugin.ExtendedExportableField

reporterField(String, String, Type, Formula.AverageMethod) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin

reporterField(String, String, Type, Formula.AverageMethod) - Static method in class net.sf.basedb.plugins.BfsExporterPlugin

reporterFields - Variable in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

ReporterFlatFileImporter - Class in net.sf.basedb.plugins

A plugin that imports reporter from a flat file.

ReporterFlatFileImporter() - Constructor for class net.sf.basedb.plugins.ReporterFlatFileImporter

Create a new importer.

ReporterFunction - Class in net.sf.basedb.util.jep

A JEP function class that adds a rep(string) or mrep(string) function to a JEP expression parser.

ReporterFunction() - Constructor for class net.sf.basedb.util.jep.ReporterFunction

Create a new instance of this function.

ReporterFunction(boolean) - Constructor for class net.sf.basedb.util.jep.ReporterFunction

Create a new instance of this function.

ReporterFunction(DbControl, RawDataType) - Constructor for class net.sf.basedb.util.jep.ReporterFunction

Create a new instance of this function working with reporters.

reporterId - Variable in class net.sf.basedb.core.data.ReporterListScoreData

reporterId - Variable in class net.sf.basedb.core.RawDataBatcher.FeatureInfo

reporterIdColumnMapping - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

reporterIdColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

reporterIdColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

reporterIndex - Variable in class net.sf.basedb.clients.web.ExperimentExplorer

The index of the current reporter on the view page.

reporterIndex - Variable in class net.sf.basedb.util.importer.spotdata.PositionEventHandler

reporterIsUsedErrorParameter - Static variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

ReporterJoiner(JoinType) - Constructor for class net.sf.basedb.core.DynamicPositionQueryJoiners.ReporterJoiner

ReporterJoiner(JoinType) - Constructor for class net.sf.basedb.core.DynamicRawDataQuery.ReporterJoiner

ReporterJoiner(JoinType) - Constructor for class net.sf.basedb.core.DynamicSpotQueryJoiners.ReporterJoiner

reporterList - Variable in class net.sf.basedb.core.data.ReporterListScoreData

reporterList - Variable in class net.sf.basedb.core.query.ReporterListExpression

reporterList - Variable in class net.sf.basedb.core.ReporterListJoin

reporterList - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

ReporterList - Class in net.sf.basedb.core

ReporterList(ReporterListData) - Constructor for class net.sf.basedb.core.ReporterList

REPORTERLIST - Enum constant in enum class net.sf.basedb.core.Item

The item is a ReporterType.

ReporterListData - Class in net.sf.basedb.core.data

This class holds information about a reporter list.

ReporterListData() - Constructor for class net.sf.basedb.core.data.ReporterListData

ReporterListExpression - Class in net.sf.basedb.core.query

Represents a property of a reporter list in a dynamic query: alias.property.

ReporterListExpression(ReporterList, String, String, String, JoinType) - Constructor for class net.sf.basedb.core.query.ReporterListExpression

ReporterListExpression(ReporterList, String, JoinType) - Constructor for class net.sf.basedb.core.query.ReporterListExpression

Create a new expression for the specified reporter list.

ReporterListJoin - Class in net.sf.basedb.core

Represents a join to a reporter list in a dynamic query: leftTable JOIN ReporterListScores ON ...

ReporterListJoin(ReporterList, JoinType, RealTable, String) - Constructor for class net.sf.basedb.core.ReporterListJoin

Create a new join to a reporter list using the given RealTable as the left table.

ReporterListJoin(ReporterList, JoinType, VirtualTable, VirtualColumn) - Constructor for class net.sf.basedb.core.ReporterListJoin

Create a new join to a reporter list using the given VirtualTable as the left table.

ReporterListJoiner(JoinType) - Constructor for class net.sf.basedb.core.DynamicPositionQueryJoiners.ReporterListJoiner

ReporterListJoiner(JoinType) - Constructor for class net.sf.basedb.core.DynamicRawDataQuery.ReporterListJoiner

ReporterListJoiner(JoinType) - Constructor for class net.sf.basedb.core.DynamicReporterQuery.ReporterListJoiner

ReporterListJoiner(JoinType) - Constructor for class net.sf.basedb.core.DynamicSpotQueryJoiners.ReporterListJoiner

ReporterListJoiner(JoinType) - Constructor for class net.sf.basedb.core.HqlQueryJoiners.ReporterListJoiner

reporterListParameter - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

reporterLists - Variable in class net.sf.basedb.core.data.ExperimentData

ReporterListScoreData - Class in net.sf.basedb.core.data

This class holds information about the score of a reporter in a reporter list.

ReporterListScoreData() - Constructor for class net.sf.basedb.core.data.ReporterListScoreData

reporterListScores - Variable in class net.sf.basedb.core.data.ReporterData

ReporterMapFlatFileImporter - Class in net.sf.basedb.plugins

A plugin that imports features to an ArrayDesign from a flat file.

ReporterMapFlatFileImporter() - Constructor for class net.sf.basedb.plugins.ReporterMapFlatFileImporter

Create a new importer.

reporterMapMember - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

reporterMapper - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter

reporterMapper - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter

reporterMapper - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

reporterMapper - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

ReporterPositions(int, int[]) - Constructor for class net.sf.basedb.clients.web.ExperimentExplorer.ReporterPositions

reporterPrefix - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter

reporterPrefixParameter - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter

ReporterPropertyExpression - Class in net.sf.basedb.core

An expression representing the property of a reporter.

ReporterPropertyExpression(String) - Constructor for class net.sf.basedb.core.ReporterPropertyExpression

Create a new reporter property expression.

ReporterPropertyExpression(String, Boolean) - Constructor for class net.sf.basedb.core.ReporterPropertyExpression

Create a new reporter property expression.

reporterProxy - Variable in class net.sf.basedb.core.RawDataBatcher

ReporterProxy() - Constructor for class net.sf.basedb.core.RawDataBatcher.ReporterProxy

ReporterProxy() - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileImporter.ReporterProxy

reporters - Variable in class net.sf.basedb.core.data.ReporterListData

REPORTERS - Static variable in class net.sf.basedb.core.RealTable

REPORTERS_INNER - Static variable in class net.sf.basedb.core.DynamicPositionQueryJoiners

This instance joins reporters with an inner join.

REPORTERS_INNER - Static variable in class net.sf.basedb.core.DynamicSpotQueryJoiners

This instance joins reporters with an inner join.

REPORTERS_LEFT - Static variable in class net.sf.basedb.core.DynamicPositionQueryJoiners

This instance joins reporters with a left join.

REPORTERS_LEFT - Static variable in class net.sf.basedb.core.DynamicSpotQueryJoiners

This instance joins reporters with a left join.

ReporterScore - Class in net.sf.basedb.core

Get information about the reporters and their score in a reporter list.

ReporterScore(ReporterListScoreData) - Constructor for class net.sf.basedb.core.ReporterScore

REPORTERSCORE - Enum constant in enum class net.sf.basedb.core.Item

The item is a ReporterScore.

ReporterScore2DataPropertyPath(Type) - Constructor for class net.sf.basedb.core.Metadata.ReporterScore2DataPropertyPath

ReporterScoreQuery - Class in net.sf.basedb.core

This is a temporary solution to query against the reporter list's score.

ReporterScoreQuery() - Constructor for class net.sf.basedb.core.ReporterScoreQuery

Create a new query for the specified item, using the default optional runtime filter.

ReporterScoreQueryWrapper - Class in net.sf.basedb.clients.web.plugins

A query wrapper for ReporterScoreQuery:s.

ReporterScoreQueryWrapper(ReporterScoreQuery) - Constructor for class net.sf.basedb.clients.web.plugins.ReporterScoreQueryWrapper

Create a new query wrapper.

ReporterScoreResultIterator - Class in net.sf.basedb.core

This is a temporary solution for returning reporter list scores as an iterator.

ReporterScoreResultIterator(ScrollIterator<ReporterListScoreData>, DbControl, long) - Constructor for class net.sf.basedb.core.ReporterScoreResultIterator

reporterType - Variable in class net.sf.basedb.core.data.ReporterData

reporterType - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

ReporterType - Class in net.sf.basedb.core

This class holds reporter type information.

ReporterType(ReporterTypeData) - Constructor for class net.sf.basedb.core.ReporterType

Constructor that sets reporter type data.

REPORTERTYPE - Enum constant in enum class net.sf.basedb.core.Item

The item is a ReporterType.

reporterTypeColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

ReporterTypeData - Class in net.sf.basedb.core.data

This class holds reporter type information.

ReporterTypeData() - Constructor for class net.sf.basedb.core.data.ReporterTypeData

Default constructor.

reporterTypeMapper - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

reporterTypeParameter - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

reporterTypes - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

reporterWriter - Variable in class net.sf.basedb.util.export.spotdata.BfsExporter

reportInterval - Variable in class net.sf.basedb.util.importer.spotdata.BfsImporter.ProgressEventHandler

reportOnly - Variable in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter

request - Variable in class net.sf.basedb.clients.web.extensions.IgnoreFilter

request - Variable in class net.sf.basedb.clients.web.extensions.InstallFilter

request - Variable in class net.sf.basedb.clients.web.extensions.UninstallFilter

request - Variable in class net.sf.basedb.core.plugin.ParameterValuesWrapper

request - Variable in class net.sf.basedb.core.PluginResponse

Request - Interface in net.sf.basedb.core.plugin

Pass request information to a plugin.

requestExternalStatusUpdate() - Method in class net.sf.basedb.core.InternalJobQueue

requestHandler - Variable in class net.sf.basedb.clients.jobagent.Agent

requestHandler - Variable in class net.sf.basedb.util.jobagent.JobAgentServerConnection.ListenerThread

requestHandler - Variable in class net.sf.basedb.util.jobagent.JobAgentServerConnection

requestHandler - Variable in class net.sf.basedb.util.jobagent.JobAgentServerConnection.RequestHandlerThread

RequestHandler - Interface in net.sf.basedb.util.jobagent

A request handler object takes care of an incoming request from a JobAgentServerConnection, processes it and returns an answer.

RequestHandlerThread(Socket, RequestHandler, Logger) - Constructor for class net.sf.basedb.util.jobagent.JobAgentServerConnection.RequestHandlerThread

RequestImpl(boolean) - Constructor for class net.sf.basedb.core.PluginRequest.RequestImpl

RequestInformation - Class in net.sf.basedb.core

Get information about the parameters the plugin needs for a particular request.

RequestInformation(String, String, String, List<PluginParameter<?>>) - Constructor for class net.sf.basedb.core.RequestInformation

RequestInformation(String, String, String, List<PluginParameter<?>>, String) - Constructor for class net.sf.basedb.core.RequestInformation

requestParameters - Variable in class net.sf.basedb.core.PluginRequest

requestStatusUpdate() - Method in class net.sf.basedb.core.Job

Request that the underlying job updates the status information about itself.

RequestWrapper - Class in net.sf.basedb.clients.web.extensions

Wrapper for HttpServletRequest that allows us to set proper servlet path and path info attributes for an extension servlet.

RequestWrapper(String, Request) - Constructor for class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper

RequestWrapper(HttpServletRequest, String, String) - Constructor for class net.sf.basedb.clients.web.extensions.RequestWrapper

required - Variable in class net.sf.basedb.clients.web.taglib.Select

If a value is required or not.

required - Variable in class net.sf.basedb.core.data.ItemSubtypeFileTypeData

required - Variable in class net.sf.basedb.core.data.PlatformFileTypeData

required - Variable in class net.sf.basedb.core.Install.ItemSubtypeFT

required - Variable in class net.sf.basedb.core.Install.PlatformFT

required - Variable in class net.sf.basedb.plugins.executor.ParameterDefinition

requiredColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

requiredColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

requiredColumnMapping - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

requiredColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

requiredColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

requiredFeatureIdColumnMapping - Static variable in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter

requiredFilter - Variable in class net.sf.basedb.core.AbstractEntityQuery

The required runtime filter.

requiredFilters - Static variable in class net.sf.basedb.core.QueryRuntimeFilterFactory

requiredForMiame - Variable in class net.sf.basedb.core.data.AnnotationTypeData

requiredRegexpType - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter

requiredSaveAsType - Static variable in class net.sf.basedb.core.plugin.AbstractExporterPlugin

requiredStringParameter - Static variable in class net.sf.basedb.plugins.PlateMappingImporter

requireEmptyDatabase - Variable in enum class net.sf.basedb.core.hibernate.SchemaGenerator.Mode

requireEmptyDatabase() - Method in enum class net.sf.basedb.core.hibernate.SchemaGenerator.Mode

Does this installation mode require an empty database or not?

requiresConfiguration - Variable in class net.sf.basedb.core.data.PluginDefinitionData

requiresConfiguration() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport

requiresConfiguration() - Method in class net.sf.basedb.core.plugin.AbstractPlugin

Returns FALSE, since that is how the plugins used to work before this method was introduced.

requiresConfiguration() - Method in interface net.sf.basedb.core.plugin.Plugin

Return TRUE if the plugin requires a configuration when executing a job.

requiresConfiguration() - Method in class net.sf.basedb.core.PluginDefinition

Check if the plugin requires a configuration to execute a job.

requiresConfiguration() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

Return TRUE, since the implementation requires it for finding the regular expressions used by the FlatFileParser.

requiresConfiguration() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter

requiresConfiguration() - Method in class net.sf.basedb.plugins.Base1PluginExecuter

requiresConfiguration() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin

requiresConfiguration() - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

requiresConfiguration() - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

requiresConfiguration() - Method in class net.sf.basedb.plugins.BfsExporterPlugin

requiresConfiguration() - Method in class net.sf.basedb.plugins.CdfFileReporterImporter

requiresConfiguration() - Method in class net.sf.basedb.plugins.CloneReportersPlugin

requiresConfiguration() - Method in class net.sf.basedb.plugins.executor.AbstractIOSupport

requiresConfiguration() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

requiresConfiguration() - Method in class net.sf.basedb.plugins.FormulaFilter

requiresConfiguration() - Method in class net.sf.basedb.plugins.GalExporter

requiresConfiguration() - Method in class net.sf.basedb.plugins.HelpExporter

requiresConfiguration() - Method in class net.sf.basedb.plugins.HelpImporter

requiresConfiguration() - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter

requiresConfiguration() - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin

requiresConfiguration() - Method in class net.sf.basedb.plugins.JepExtraValueCalculator

requiresConfiguration() - Method in class net.sf.basedb.plugins.JepIntensityTransformer

requiresConfiguration() - Method in class net.sf.basedb.plugins.LowessNormalization

requiresConfiguration() - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator

requiresConfiguration() - Method in class net.sf.basedb.plugins.ManualTransformCreator

requiresConfiguration() - Method in class net.sf.basedb.plugins.MedianRatioNormalization

requiresConfiguration() - Method in class net.sf.basedb.plugins.PackedFileExporter

requiresConfiguration() - Method in class net.sf.basedb.plugins.PlateFlatFileImporter

requiresConfiguration() - Method in class net.sf.basedb.plugins.PlateMappingExporter

requiresConfiguration() - Method in class net.sf.basedb.plugins.PlateMappingImporter

requiresConfiguration() - Method in class net.sf.basedb.plugins.PluginConfigurationExporter

Always false

requiresConfiguration() - Method in class net.sf.basedb.plugins.PluginConfigurationImporter

requiresConfiguration() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter

requiresConfiguration() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter

requiresConfiguration() - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter

requiresConfiguration() - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

requiresConfiguration() - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker

Returns FALSE.

reset() - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup

Resets all collected statistics in this group.

reset() - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary

Reset the collected statistics in all annotation groups.

reset() - Method in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream

Not supported.

reset() - Static method in class net.sf.basedb.clients.web.servlet.RssNewsFeed

Reset the feed and force it to regenerate it's content.

reset() - Method in class net.sf.basedb.clients.web.util.ProjectSpecificInfoFilter

Reset the flags to false.

reset() - Method in class net.sf.basedb.core.AbstractHqlQuery

Reset all non-permanent query elements of the query and clear cached queries.

reset() - Method in class net.sf.basedb.core.AbstractQuery

Resets the query, allowing you to add more restrictions, joins, order objects and parameters.

reset() - Method in class net.sf.basedb.core.DiskUsageStatistics

Reset the internal cache of already loaded statistics.

reset() - Method in class net.sf.basedb.core.DynamicPositionQuery

Reset join information.

reset() - Method in class net.sf.basedb.core.DynamicSpotQuery

Reset join information.

reset() - Method in interface net.sf.basedb.core.query.Query

Reset the query, removing all non-permanent query elements and parameter values.

reset() - Method in class net.sf.basedb.util.gtf.GtfInputStream

reset() - Method in class net.sf.basedb.util.InputStreamSplitter

reset() - Method in class net.sf.basedb.util.InputStreamTracker

reset(int) - Method in class net.sf.basedb.util.timer.PerformanceTimer

Reset a timer.

reset(DbControl) - Method in class net.sf.basedb.util.overview.GenericOverview

Reset the overview and re-create the root node.

reset(DynamicPositionQuery) - Method in class net.sf.basedb.core.DynamicPositionQueryJoiners.ExtraValueJoiner

reset(DynamicPositionQuery) - Method in class net.sf.basedb.core.DynamicPositionQueryJoiners.ReporterJoiner

reset(DynamicPositionQuery) - Method in class net.sf.basedb.core.DynamicPositionQueryJoiners.ReporterListJoiner

reset(DynamicRawDataQuery) - Method in class net.sf.basedb.core.DynamicRawDataQuery.RawBioAssayJoiner

reset(DynamicRawDataQuery) - Method in class net.sf.basedb.core.DynamicRawDataQuery.ReporterJoiner

reset(DynamicRawDataQuery) - Method in class net.sf.basedb.core.DynamicRawDataQuery.ReporterListJoiner

reset(DynamicReporterQuery) - Method in class net.sf.basedb.core.DynamicReporterQuery.MasterReporterJoiner

reset(DynamicReporterQuery) - Method in class net.sf.basedb.core.DynamicReporterQuery.ReporterListJoiner

reset(DynamicSpotQuery) - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.ExtraValueJoiner

reset(DynamicSpotQuery) - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.RawDataJoiner

reset(DynamicSpotQuery) - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.ReporterJoiner

reset(DynamicSpotQuery) - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.ReporterListJoiner

reset(Response.Status) - Method in class net.sf.basedb.core.PluginResponse

reset(HqlQuery) - Method in class net.sf.basedb.core.HqlQueryJoiners.AnnotationJoiner

reset(HqlQuery) - Method in class net.sf.basedb.core.HqlQueryJoiners.ReporterListJoiner

reset(Q) - Method in interface net.sf.basedb.core.query.AutoJoiner

Called to indicate that Query.reset() has been called on the given query.

resetAll() - Method in class net.sf.basedb.util.timer.PerformanceTimer

Reset all timers.

resetCache() - Method in class net.sf.basedb.util.units.UnitCache

Clear the cache of all units.

resetClassLoader - Variable in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor

resetClassLoader() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile

Reset the classloader for this file, forcing a new instance in case the JAR file has been changed.

resetCollected() - Method in class net.sf.basedb.util.listable.CollectExtracts

Clear all collected extracts in order to prepare for a new collection.

resetCollected() - Method in class net.sf.basedb.util.listable.TransformContext

Clear all collected items and disable both 'collecting' and 'avoiding'.

ResetCollected(SourceItemTransformer) - Constructor for class net.sf.basedb.util.listable.CollectExtracts.ResetCollected

resetDynamicAttributes() - Method in class net.sf.basedb.clients.web.taglib.StylableTag

Clear all dynamic attributes.

resetErrorFlag - Variable in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor

resetMetadata() - Method in class net.sf.basedb.util.affymetrix.CdfValidationAction

resetMetadata() - Method in class net.sf.basedb.util.affymetrix.CelValidationAction

resetMetadata() - Method in interface net.sf.basedb.util.fileset.ValidationAction

Reset all metadata that this class normally can set.

resetMetadata() - Method in class net.sf.basedb.util.gtf.GtfValidationAction

resetMetadata(ArrayDesign) - Method in class net.sf.basedb.util.affymetrix.CdfValidator

Reset metadata on the given array design.

resetMetadata(RawBioAssay) - Method in class net.sf.basedb.util.affymetrix.CelValidator

Reset metadata on the given raw bioassay.

ResetMetadataRenderer - Class in net.sf.basedb.util.fileset

Renderer implementation for resetting metadata for the members of a file set.

ResetMetadataRenderer(List<ValidatingFileSetMember>) - Constructor for class net.sf.basedb.util.fileset.ResetMetadataRenderer

Create a new renderer instance.

ResetProcessor - Class in net.sf.basedb.util.extensions.manager.processor

File processor implementation that reset the error flag, class loader, etc.

ResetProcessor(ProcessResults) - Constructor for class net.sf.basedb.util.extensions.manager.processor.ResetProcessor

Create a new processor instance using default settings.

resetTemporary() - Method in class net.sf.basedb.core.AbstractQuery

RESISTANCE - Static variable in class net.sf.basedb.core.Quantity

The id for the Quantity object representing electrical resistance.

resolveEntity(String, String) - Method in class net.sf.basedb.util.XmlUtil2.Validator

This method is called when the parser wants a reference to the DTD file.

resolvePath(String, String) - Static method in class net.sf.basedb.plugins.batchimport.FileImporter

resource - Variable in class net.sf.basedb.util.uri.CloseResourceInputStream

ResourceBundleFactory - Class in net.sf.basedb.util.resources

Factory for loading resource bundles.

ResourceBundleFactory() - Constructor for class net.sf.basedb.util.resources.ResourceBundleFactory

ResourceBundleWrapper - Class in net.sf.basedb.util.resources

A wrapper around ResourceBundle objects.

ResourceBundleWrapper(String, ResourceBundle) - Constructor for class net.sf.basedb.util.resources.ResourceBundleWrapper

The wrapper is created by ResourceBundleFactory.

RESOURCES_URL - Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl

The location where the extensions resources are extracted.

RESOURCES_URL - Static variable in class net.sf.basedb.clients.web.extensions.XJspCompiler

The location where the extensions resources are extracted.

resourcesPath - Variable in class net.sf.basedb.clients.web.extensions.WebClientRegisterExtensionsProcessor

response - Variable in class net.sf.basedb.clients.web.util.ServletExportOutputStream

response - Variable in class net.sf.basedb.core.PluginResponse

Response - Interface in net.sf.basedb.core.plugin

The response interface used by the core.

Response.Status - Enum Class in net.sf.basedb.core.plugin

responseFilter - Variable in class net.sf.basedb.util.uri.http.HttpConnectionManager

ResponseFilter() - Constructor for class net.sf.basedb.util.GeoLocation.ResponseFilter

ResponseImpl() - Constructor for class net.sf.basedb.core.PluginResponse.ResponseImpl

ResponseWrapper() - Constructor for class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper

restart(Extension<ServiceControllerAction>) - Static method in class net.sf.basedb.clients.web.extensions.service.Services

Restart services as a result of an administrator has uninstalled an extension or is updating/disabling an existing on.

restorePath(Directory) - Static method in class net.sf.basedb.util.RemovableUtil

Restores the path to a directory

restrict(Restriction) - Method in class net.sf.basedb.core.AbstractQuery

restrict(Restriction) - Method in interface net.sf.basedb.core.query.Query

Add a restriction query element to the restriction list.

RESTRICTED_WRITE - Enum constant in enum class net.sf.basedb.core.Permission

This permission allows a user to update some information about an item.

restrictedEdit - Variable in class net.sf.basedb.core.ExtendedProperty

restriction(String, String) - Static method in class net.sf.basedb.core.query.Hql

Restriction - Interface in net.sf.basedb.core.query

A restriction query element.

restrictions - Variable in class net.sf.basedb.core.AbstractQuery

List of restrictions added to the query.

restrictions - Variable in class net.sf.basedb.core.ItemContext.RowRestrictions

restrictions - Variable in class net.sf.basedb.core.query.AndRestriction

restrictions - Variable in class net.sf.basedb.core.query.OrRestriction

Restrictions - Class in net.sf.basedb.core.query

A factory class to create restrictions.

Restrictions() - Constructor for class net.sf.basedb.core.query.Restrictions

RestrictionTransformer - Class in net.sf.basedb.util.listable

Transformer implementation that is intended to provide a final filtering of target items.

RestrictionTransformer(SourceItemTransformer, ItemQuery<?>) - Constructor for class net.sf.basedb.util.listable.RestrictionTransformer

Create a new transformer and use the given query to find the target items.

RestrictionTransformer(SourceItemTransformer, Restriction) - Constructor for class net.sf.basedb.util.listable.RestrictionTransformer

Create a new transformer and apply the given restriction to items before they are returned.

restrictPermanent(Restriction) - Method in class net.sf.basedb.core.AbstractQuery

restrictPermanent(Restriction) - Method in interface net.sf.basedb.core.query.Query

Permanently add a restriction query element to the restriction list.

restrictSource(DynamicSpotQuery, List<BioAssay>) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

Restricts a query to only include values from listed bioassays

restrictToPushAnnotationSubtypes(ItemQuery<? extends Subtypable>) - Static method in class net.sf.basedb.util.overview.OverviewUtil

Add a restriction to the query that limit the returned result to those items that has a subtype with the ItemSubtype.getPushAnnotations() flag set.

result - Variable in class net.sf.basedb.util.jep.ChannelFunction

result - Variable in class net.sf.basedb.util.jep.ExtraValueFunction

result - Variable in class net.sf.basedb.util.jep.RawChannelFunction

result - Variable in class net.sf.basedb.util.jep.ScoreFunction

result - Variable in class net.sf.basedb.util.parser.FlatFileParser.Data

resultIntensityTransform - Variable in class net.sf.basedb.core.data.FormulaData

ResultIterator<I> - Interface in net.sf.basedb.core.query

Return the result of a query as an iterator.

ResultList<I> - Interface in net.sf.basedb.core.query

Return the result of a query as a list.

ResultListIterator(Iterator<? extends BasicData>, Class<T>) - Constructor for class net.sf.basedb.core.ItemResultList.ResultListIterator

ResultListListIterator(ListIterator<? extends BasicData>, Class<T>) - Constructor for class net.sf.basedb.core.ItemResultList.ResultListListIterator

results - Variable in class net.sf.basedb.clients.web.extensions.InstalledFileProcessor

results - Variable in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor

results - Variable in class net.sf.basedb.clients.web.extensions.UninstalledFileProcessor

results - Variable in class net.sf.basedb.core.DynamicResultIterator

The results of the query.

results - Variable in class net.sf.basedb.core.ScrollIterator

results - Variable in class net.sf.basedb.util.extensions.manager.filter.WasProcessedFilter

results - Variable in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor

results - Variable in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor

results - Variable in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor

results - Variable in class net.sf.basedb.util.extensions.manager.processor.IgnoreFileProcessor

results - Variable in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor

results - Variable in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor

results - Variable in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor

results - Variable in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor

ResultSetWork<R> - Class in net.sf.basedb.core.hibernate

A work implementation that executes an SQL query on the connection, and returns a value that is picked by a subclass from the resulting ResultSet.

ResultSetWork(SessionControl, String) - Constructor for class net.sf.basedb.core.hibernate.ResultSetWork

Create a new work item.

ResultWriter - Interface in net.sf.basedb.core.migrate

Interface for quick writing of data from a JDBC result set to a writer.

ResultWriterFactory - Interface in net.sf.basedb.core.migrate

Interface for factories that knows how to create result writers.

ResumableConnectionManager - Interface in net.sf.basedb.util.uri

An extension to the ConnectionManager interface that add support for specifying a start offset when downloading the external file.

resync - Variable in class net.sf.basedb.util.annotations.InheritSpecification

resyncCloned() - Method in class net.sf.basedb.core.Annotation

If this is a cloned annotation, resync the cloned values.

resyncFilter - Variable in class net.sf.basedb.util.annotations.InheritAnnotationsManager

resyncFilter(DbControl, ItemList.SynchronizeOption, boolean, ProgressReporter) - Method in class net.sf.basedb.core.ItemList

Re-sync with the current synchronization filter.

retainAll(Collection<?>) - Method in class net.sf.basedb.core.AbstractResultList

Not supported.

retainAll(Collection<?>) - Method in class net.sf.basedb.core.UnmodifiableResultList

Not supported.

retainAll(Collection<?>) - Method in class net.sf.basedb.util.Tree

Not supported.

retainAll(ItemList) - Method in class net.sf.basedb.core.ItemList

Remove all items from this list that are NOT present in the other list.

retainAll(ItemList.DelayedAdditionManager) - Method in class net.sf.basedb.core.ItemList.DelayedAdditionManager

retainAll(ReporterList) - Method in class net.sf.basedb.core.ReporterList

Remove all reporters from this list that are NOT present in the other list.

retainIfPresentIn(int, int, Collection<ItemList>) - Method in class net.sf.basedb.core.ItemList

Retain items that are present in the specified number of lists in this list.

retainIfPresentIn(int, int, Collection<ReporterList>) - Method in class net.sf.basedb.core.ReporterList

Retain reporters that are present in the specified number of lists in this list.

retainIntersection(Collection<ItemList>) - Method in class net.sf.basedb.core.ItemList

Retain items that are present in ALL OF the given lists in this list.

retainIntersection(Collection<ReporterList>) - Method in class net.sf.basedb.core.ReporterList

Retain reporters that are present in ALL OF the given lists in this list.

retainMembers(Set<Integer>, ItemList.DelayedAdditionManager) - Method in class net.sf.basedb.core.ItemList

Keep only specified members in this list

retainReporters(Set<Integer>) - Method in class net.sf.basedb.core.ReporterList

retainUnion(Collection<ItemList>) - Method in class net.sf.basedb.core.ItemList

Retain items that are present in at least ONE OF the given lists in this list.

retainUnion(Collection<ReporterList>) - Method in class net.sf.basedb.core.ReporterList

Retain reporters that are present in at least ONE OF the given lists in this list.

RethrowErrorHandlerFactory - Class in net.sf.basedb.util.extensions

Extension to the logging error handler factory that create error handlers that re-throw the original exception.

RethrowErrorHandlerFactory() - Constructor for class net.sf.basedb.util.extensions.RethrowErrorHandlerFactory

retry(boolean, boolean) - Method in class net.sf.basedb.core.Job

Retry a job which finished with an error or a successful dry-run job.

returnArray - Variable in class net.sf.basedb.core.ScrollIterator

returnClass - Variable in class net.sf.basedb.core.query.ReturnClassFilter

ReturnClassFilter - Class in net.sf.basedb.core.query

Filter implementation that checks if the items returned by a EntityQuery are compatible with the specified class.

ReturnClassFilter(Class<?>) - Constructor for class net.sf.basedb.core.query.ReturnClassFilter

Creates a filter that matches the specified item class.

returnedRows - Variable in class net.sf.basedb.core.DynamicResultIterator

returnKeys - Variable in class net.sf.basedb.util.resources.ResourceBundleWrapper

returnTotalCount - Variable in class net.sf.basedb.core.AbstractQuery

If the query should calculate the total number of matching items in the case that limits have been set with AbstractQuery.firstResult or AbstractQuery.maxResults.

returnType - Variable in class net.sf.basedb.core.AbstractEntityQuery

The item type returned by the query, eg.

REVERSE - Enum constant in enum class net.sf.basedb.util.overview.node.ChildNodeDirection

Child nodes should be loaded in the reverse-loading direction.

right - Variable in class net.sf.basedb.core.DynamicJoin

right - Variable in class net.sf.basedb.core.ExtraValueJoin

right - Variable in class net.sf.basedb.core.RealJoin

right - Variable in class net.sf.basedb.core.ReporterListJoin

rightColumns - Variable in class net.sf.basedb.core.DynamicJoin

rightJoin(String, String) - Static method in class net.sf.basedb.core.query.Hql

Same as rightJoin(null, propert, joinedAlias, null)

rightJoin(String, String, String, Restriction) - Static method in class net.sf.basedb.core.query.Hql

Create a right join query element.

rLeft - Variable in class net.sf.basedb.core.RealJoin

rLeftColumn - Variable in class net.sf.basedb.core.RealJoin

rlike(String, String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine

Return <value> = <regexp>

rlike(String, String) - Method in interface net.sf.basedb.core.dbengine.DbEngine

Get a function/expression that matches the left value against the right value which should be a regular expression.

rlike(String, String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine

Return <value> RLIKE <regexp>.

rlike(String, String) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine

Return <value> ~ <regexp>.

rlike(Expression, Expression) - Static method in class net.sf.basedb.core.query.Restrictions

Check if an expression matches a regular expression.

RLIKE - Enum constant in enum class net.sf.basedb.core.Operator

RlikeRestriction - Class in net.sf.basedb.core.query

Checks if an expression matches a regular expression: e RLIKE regexp (MySQL) or e ~ regexp (Postgres).

RlikeRestriction(Expression, Expression) - Constructor for class net.sf.basedb.core.query.RlikeRestriction

robotHasBeenSet - Variable in class net.sf.basedb.core.ArrayBatch

role - Variable in class net.sf.basedb.core.data.BioPlateEventParticipantData

Role - Class in net.sf.basedb.core

This class is used to represent roles.

Role(RoleData) - Constructor for class net.sf.basedb.core.Role

ROLE - Enum constant in enum class net.sf.basedb.core.Item

The item is a Role.

Role.QueryRuntimeFilterImpl - Class in net.sf.basedb.core

A runtime filter implementation that limits a query to only return roles where the logged in user is a member unless the logged in user has generic read permission.

RoleData - Class in net.sf.basedb.core.data

This class holds information about a role.

RoleData() - Constructor for class net.sf.basedb.core.data.RoleData

roleId - Variable in class net.sf.basedb.core.data.keyring.RoleKeys

roleId - Variable in class net.sf.basedb.core.data.keyring.UserRoles

RoleKey - Class in net.sf.basedb.core

This class is used to represent a role key.

RoleKey(RoleKeyData) - Constructor for class net.sf.basedb.core.RoleKey

ROLEKEY - Enum constant in enum class net.sf.basedb.core.Item

The item is a RoleKey.

RoleKeyData - Class in net.sf.basedb.core.data

This class holds information access privileges for roles.

RoleKeyData() - Constructor for class net.sf.basedb.core.data.RoleKeyData

roleKeys - Static variable in class net.sf.basedb.core.SystemItems

An array to hold mappings for RoleKeyData: RoleKeyData.itemType --> RoleKeyData.id

RoleKeys - Class in net.sf.basedb.core.data.keyring

Class for mapping the RoleKeys table.

RoleKeys() - Constructor for class net.sf.basedb.core.data.keyring.RoleKeys

Create a new RoleKeys object.

rolePermissions - Variable in class net.sf.basedb.core.Keyring

Two-dimensional array for holding the permissions for RoleKey:s.

roles - Variable in class net.sf.basedb.core.data.RoleKeyData

roles - Variable in class net.sf.basedb.core.data.UserData

roles - Variable in class net.sf.basedb.core.Keyring

Holds the ID of all roles that the user is a member of.

rollback() - Method in class net.sf.basedb.core.DbControl

Rollback the transaction.

rollback(Transaction) - Static method in class net.sf.basedb.core.HibernateUtil

Rollback a transaction.

rollbackToSavepoint(Connection, Savepoint, String) - Method in class net.sf.basedb.core.AbstractSqlQuery

Rollback the current transaction to the given savepoint.

root - Variable in class net.sf.basedb.util.extensions.xml.PathConverter

root - Variable in class net.sf.basedb.util.StaticCache

root - Variable in class net.sf.basedb.util.Tree

ROOT - Static variable in class net.sf.basedb.clients.web.taglib.menu.Menu

The path to the root directory of this webserver.

ROOT - Static variable in class net.sf.basedb.clients.web.taglib.Page

The path to the root directory of this webserver.

ROOT - Static variable in class net.sf.basedb.clients.web.taglib.path.Path

The path to the root directory of this webserver.

ROOT - Variable in class net.sf.basedb.clients.web.taglib.PropertyValue

ROOT - Static variable in class net.sf.basedb.core.Directory

The id for the Directory item representing the root.

ROOT - Static variable in class net.sf.basedb.core.Keyring

ROOT - Static variable in class net.sf.basedb.core.User

The system id for the User representing the root account.

ROOT - Static variable in class net.sf.basedb.plugins.batchimport.FileImporter.PathIdMethod

ROOT() - Static method in class net.sf.basedb.clients.web.taglib.Page

Static version of Page.getRoot().

rootAlias - Variable in class net.sf.basedb.core.AbstractHqlQuery

The alias for the root table.

rootAlias - Variable in class net.sf.basedb.core.DynamicReporterQuery

rootDerivedBioAssays - Variable in class net.sf.basedb.core.data.PhysicalBioAssayData

rootEntity - Variable in class net.sf.basedb.core.AbstractQuery

The root enitity.

rootItem - Variable in class net.sf.basedb.util.overview.GenericOverview

rootNode - Variable in class net.sf.basedb.util.overview.GenericOverview

rootPath - Variable in class net.sf.basedb.core.data.FileServerData

rootPath - Variable in class net.sf.basedb.plugins.batchimport.FileImporter.PathIdMethod

rootPath - Variable in class net.sf.basedb.plugins.batchimport.FileImporter

rootPath - Variable in class net.sf.basedb.util.StaticCache

rootPath - Variable in class net.sf.basedb.util.uri.ConnectionParameters

RootRawBioAssay - Class in net.sf.basedb.core

Represents the use of a raw bioassay in an experiment.

RootRawBioAssay(RootRawBioAssayData) - Constructor for class net.sf.basedb.core.RootRawBioAssay

Creates a new root raw bioassay item from the given data.

ROOTRAWBIOASSAY - Enum constant in enum class net.sf.basedb.core.Item

The item is a RootRawBioAssay.

RootRawBioAssayData - Class in net.sf.basedb.core.data

This class holds the link between experiments and raw bioassays including an annotation set that is representing the experimental factor values.

RootRawBioAssayData() - Constructor for class net.sf.basedb.core.data.RootRawBioAssayData

RootRawBioAssayLoader - Class in net.sf.basedb.util.overview.loader

Node loader implementation for root raw bioassays.

RootRawBioAssayLoader() - Constructor for class net.sf.basedb.util.overview.loader.RootRawBioAssayLoader

rootRawBioAssays - Variable in class net.sf.basedb.core.data.ExperimentData

rootTable - Variable in class net.sf.basedb.core.DynamicQuery

rootTable - Variable in class net.sf.basedb.core.DynamicRawDataQuery

rootType - Variable in class net.sf.basedb.core.AbstractEntityQuery

The root item type we start with in the query. eq.

row - Variable in class net.sf.basedb.clients.web.taglib.table.PropertyFilter

row - Variable in class net.sf.basedb.core.data.BioWellData

row - Variable in class net.sf.basedb.core.data.FeatureData

row - Variable in class net.sf.basedb.core.data.MappingCoordinate

The row number.

row - Variable in class net.sf.basedb.core.data.PlateCoordinate

The row number.

row - Variable in class net.sf.basedb.core.data.RawData

row - Variable in class net.sf.basedb.core.data.WellData

row - Variable in class net.sf.basedb.core.FeatureCoordinate

The row of this feature.

Row - Class in net.sf.basedb.clients.web.taglib.table

This tag defines a new row in the table.

Row() - Constructor for class net.sf.basedb.clients.web.taglib.table.Row

rowclass - Static variable in class net.sf.basedb.clients.web.taglib.table.Table

The class names for even and odd row respectively.

rowColumnMapping - Static variable in class net.sf.basedb.plugins.PlateFlatFileImporter

rowColumnMapping - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

rowColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

rowIdList - Variable in class net.sf.basedb.core.ItemContext.RowRestrictions

rowIndex - Variable in class net.sf.basedb.core.ItemContext.RowRestrictions

rowIndex - Variable in class net.sf.basedb.core.PropertyFilter

rowIndex - Variable in class net.sf.basedb.util.bfs.AnnotationModel

rowMapper - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter

rowMapper - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

rowMapper - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

rowNo - Variable in class net.sf.basedb.util.excel.XlsxTableWriter

rowNum - Variable in class net.sf.basedb.clients.web.plugins.XlsxTemplate

rowOffset - Variable in class net.sf.basedb.util.parser.FlatFileParser.ExcelData

rowRestrictions - Variable in class net.sf.basedb.core.ItemContext.QueryRestrictions

RowRestrictions(int) - Constructor for class net.sf.basedb.core.ItemContext.RowRestrictions

rows - Variable in class net.sf.basedb.core.data.PlateGeometryData

Rows - Class in net.sf.basedb.clients.web.taglib.table

This tag is a place-holder for <tbl:row> tags.

Rows() - Constructor for class net.sf.basedb.clients.web.taglib.table.Rows

rowSeparator - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil

rowsPerPage - Variable in class net.sf.basedb.clients.web.taglib.table.Navigator

The number of rows to display on a single page.

rowsPerPage - Variable in class net.sf.basedb.core.data.ContextData

rowsPerPage - Variable in class net.sf.basedb.core.ItemContext

rs - Variable in class net.sf.basedb.core.migrate.AbstractResultWriter

RssNewsFeed - Class in net.sf.basedb.clients.web.servlet

A servlet that generates a RSS feed from the public news on the BASE server.

RssNewsFeed() - Constructor for class net.sf.basedb.clients.web.servlet.RssNewsFeed

rule - Variable in class net.sf.basedb.util.overview.extensions.ReflectValidationRuleActionFactory

rule - Variable in class net.sf.basedb.util.overview.Failure

ruleDenied - Variable in class net.sf.basedb.util.overview.validator.BasicNodeValidator

ruleMissing - Variable in class net.sf.basedb.util.overview.validator.BasicNodeValidator

run() - Method in class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor.StreamRedirector

run() - Method in class net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor.ShutdownHook

run() - Method in class net.sf.basedb.clients.jobagent.JobQueueChecker

run() - Method in class net.sf.basedb.clients.jobagent.JobRunner

Find a free slot to use and then pass control to the JobExecutor.executeJob(SessionControl, Agent, Job, JobAgentSettings, Job.ExecutionTime) method.

run() - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlotTimeoutChecker

run() - Method in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager.RemoteSlotPinger

run() - Method in class net.sf.basedb.core.Application.DbCleaner

run() - Method in class net.sf.basedb.core.Application.SessionControlCacheCleaner

run() - Method in class net.sf.basedb.core.DbControl.State

run() - Method in class net.sf.basedb.core.File.CharsetTesterThread

Runs in a separate thread.

run() - Method in class net.sf.basedb.core.InternalJobQueue.JobRunner

Execute the job.

run() - Method in class net.sf.basedb.core.InternalJobQueue

Check the database for jobs that are waiting to be executed.

run() - Method in class net.sf.basedb.core.Keyring.ReloadTask

run() - Method in class net.sf.basedb.core.PluginExecutionRequest

run() - Method in class net.sf.basedb.core.signal.SocketSignalReceiver.ListenerThread

run() - Method in class net.sf.basedb.util.annotations.RunnableInheritAnnotationsManager

run() - Method in class net.sf.basedb.util.FileCopyRunnable

run() - Method in class net.sf.basedb.util.jobagent.JobAgentServerConnection.ListenerThread

run() - Method in class net.sf.basedb.util.jobagent.JobAgentServerConnection.RequestHandlerThread

run() - Method in class net.sf.basedb.util.StaticCache.CleanupTask

run() - Method in class net.sf.basedb.util.StaticCache.State

run() - Method in class net.sf.basedb.util.timer.ThreadTimerTask

run() - Method in class net.sf.basedb.util.uri.http.HttpConnectionManager.TimeoutTimer

run(Stack) - Method in class net.sf.basedb.util.jep.ChannelFunction

run(Stack) - Method in class net.sf.basedb.util.jep.ExtraValueFunction

run(Stack) - Method in class net.sf.basedb.util.jep.FunctionSafeJep.UnknownFunction

run(Stack) - Method in class net.sf.basedb.util.jep.InReporterListFunction

run(Stack) - Method in class net.sf.basedb.util.jep.LeftFunction

run(Stack) - Method in class net.sf.basedb.util.jep.Log2Function

run(Stack) - Method in class net.sf.basedb.util.jep.MeanFunction

run(Stack) - Method in class net.sf.basedb.util.jep.NotInReporterListFunction

run(Stack) - Method in class net.sf.basedb.util.jep.PositionFunction

run(Stack) - Method in class net.sf.basedb.util.jep.RawChannelFunction

run(Stack) - Method in class net.sf.basedb.util.jep.RawFunction

run(Stack) - Method in class net.sf.basedb.util.jep.ReporterFunction

run(Stack) - Method in class net.sf.basedb.util.jep.ScoreFunction

run(Stack) - Method in class net.sf.basedb.util.jep.SimpleJepFunction

run(Stack) - Method in class net.sf.basedb.util.parser.ColFunction

run(Stack) - Method in class net.sf.basedb.util.parser.DataNoFunction

run(Stack) - Method in class net.sf.basedb.util.parser.DefaultItemFunction

run(Stack) - Method in class net.sf.basedb.util.parser.LineNoFunction

run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin

Checks the AbstractExporterPlugin.SAVE_AS parameter for the path to save the exported data.

run(Request, Response, ProgressReporter) - Method in interface net.sf.basedb.core.plugin.Plugin

Run the plugin.

run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

Implements the Request.COMMAND_EXECUTE command.

run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.Base1PluginExecuter

run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.BfsExporterPlugin

run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.CdfFileReporterImporter

run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.CloneReportersPlugin

run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.executor.AbstractIOSupport

Accepts the IOSupport.COMMAND_EXECUTE_IO_JOB command.

run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.FormulaFilter

run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.HelpImporter

run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin

run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.JepExtraValueCalculator

run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.JepIntensityTransformer

run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.LowessNormalization

run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator

run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.ManualTransformCreator

run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.MedianRatioNormalization

run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.PluginConfigurationImporter

run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker

RUN_PLUGIN - Enum constant in enum class net.sf.basedb.core.Job.Type

The job is executed by a plugin.

runExporter(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

Execute the exporter plug-in using the supplied parameters.

runExternalProgram(String, String, File, String, String, ProgressReporter) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

Run the external program.

runImporter(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

Execute the importer plug-in using the supplied parameters.

RunnableInheritAnnotationsManager - Class in net.sf.basedb.util.annotations

Utility class for processing multiple items with a InheritAnnotationsManager in a separated thread with progress reporting.

RunnableInheritAnnotationsManager(SessionControl) - Constructor for class net.sf.basedb.util.annotations.RunnableInheritAnnotationsManager

Create a new instance that should use the given session control.

runners - Variable in class net.sf.basedb.core.InternalJobQueue

Holds all currently executing jobs.

runnersGroup - Variable in class net.sf.basedb.clients.jobagent.Agent

The group were all job runners are placed.

runnersGroup - Variable in class net.sf.basedb.core.InternalJobQueue

The group were all job runners are placed.

running - Variable in class net.sf.basedb.clients.web.extensions.service.DummyService

RUNTIME_FILTER - Static variable in class net.sf.basedb.core.AnnotationSet

This filter gives everybody read permission to annotations.

RUNTIME_FILTER - Static variable in class net.sf.basedb.core.ArrayDesignPlate

This filter will only return items if the logged in user has generic read permission to array designs.

RUNTIME_FILTER - Static variable in class net.sf.basedb.core.ClientDefaultSetting

This filter will only return items if the logged in user has generic read permission to clients.

RUNTIME_FILTER - Static variable in class net.sf.basedb.core.FileSet

This filter gives everybody read permission to file sets.

RUNTIME_FILTER - Static variable in class net.sf.basedb.core.FileSetMember

This filter gives everybody read permission to file set members.

RUNTIME_FILTER - Static variable in class net.sf.basedb.core.Group

This filter will limit a query to only return groups where the logged in user is a member unless the logged in user has generic read permission.

RUNTIME_FILTER - Static variable in class net.sf.basedb.core.Help

This filter will only return items if the logged in user has generic read permission to clients.

RUNTIME_FILTER - Static variable in class net.sf.basedb.core.ItemSubtypeFileType

This filter will only return items if the logged in user has generic read permission to item subtypes.

RUNTIME_FILTER - Static variable in class net.sf.basedb.core.JobAgentSettings

This filter will only return items if the logged in user has generic read permission to job agents.

RUNTIME_FILTER - Static variable in class net.sf.basedb.core.Message

This filter will limit a query to only return messages for the logged in user unless the logged in user has generic read permission.

RUNTIME_FILTER - Static variable in class net.sf.basedb.core.News

This filter limits the returned news items to those where todays date falls between the start and end dates unless the logged in user has generic read permission.

RUNTIME_FILTER - Static variable in class net.sf.basedb.core.PlateEvent

This filter will only return items if the logged in user has generic read permission to plates.

RUNTIME_FILTER - Static variable in class net.sf.basedb.core.PlateEventType

This filter will only return items if the logged in user has generic read permission to plate types.

RUNTIME_FILTER - Static variable in class net.sf.basedb.core.PlatformFileType

This filter will only return items if the logged in user has generic read permission to platforms.

RUNTIME_FILTER - Static variable in class net.sf.basedb.core.PlatformVariant

This filter will only return items if the logged in user has generic read permission to platforms.

RUNTIME_FILTER - Static variable in class net.sf.basedb.core.Project

This filter will limit a query to only return projects where the logged in user is a member or owner unless the logged in user has generic read permission.

RUNTIME_FILTER - Static variable in class net.sf.basedb.core.Quota

This filter will only return the logged in user's quota unless the logged in user has generic read permission.

RUNTIME_FILTER - Static variable in class net.sf.basedb.core.Role

This filter will limit a query to only return roles where the logged in user is a member unless the logged in user has generic read permission.

RUNTIME_FILTER - Static variable in class net.sf.basedb.core.RoleKey

This filter will only return items if the logged in user has generic read permission to roles.

RUNTIME_FILTER - Static variable in class net.sf.basedb.core.Session

This filter will limit a query to only return sessions for the logged in user unless the logged in user has generic read permission.

RUNTIME_FILTER - Static variable in class net.sf.basedb.core.User

This filter will limit a query to only return users which are members of at least one of the groups where the logged in user is a member unless the logged in user has generic read permission.

RUNTIME_FILTER - Static variable in class net.sf.basedb.core.UserDefaultSetting

This filter will only return items if the logged in user has generic read permission to users.

RUNTIME_FILTER - Static variable in class net.sf.basedb.core.UserDevice

This filter will limit a query to only return devices for the logged in user unless the logged in user has generic read permission.

rwLock - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile

rwLock - Variable in class net.sf.basedb.util.StaticCache.LockEntry

S

s - Variable in class net.sf.basedb.core.QueryExecutor.CancelableStatement

S - Variable in class net.sf.basedb.util.bcrypt.BCrypt

S_orig - Static variable in class net.sf.basedb.util.bcrypt.BCrypt

SAFE_TAGS - Static variable in class net.sf.basedb.clients.web.util.HTML

This pattern is a list of HTML tags considered "safe".

safeEquals(Date, Date, boolean) - Static method in class net.sf.basedb.core.DateUtil

Compare two date instances for equality while protecting from strange implementations in the java.util.Date and java.sql.Timestamp classes.

SafeFunctionTable(FunctionSafeJep) - Constructor for class net.sf.basedb.util.jep.FunctionSafeJep.SafeFunctionTable

safeIdList(DbControl, ItemQuery<?>, String, Set<Integer>) - Method in class net.sf.basedb.util.listable.AbstractSourceItemTransformer

Safely execute the query even if the number of values in the 'values' set is higher than DbEngine.getMaxParametersInQuery().

safeInvariantEquals(List<Date>, List<Date>, boolean) - Static method in class net.sf.basedb.core.DateUtil

Checks if two lists contains equal elements disregarding their positions in the array.

safeToDrop(TableInfo.IndexInfo) - Method in class net.sf.basedb.core.dbengine.TableInfo

It is safe to drop an index if it is not the primary key.

SAM - Static variable in class net.sf.basedb.core.DataFileType

The external ID for the file type representing a SAM (Sequence Alignment/Map) file.

SAME_UNITS - Static variable in class net.sf.basedb.clients.web.plugins.SimpleExport

sameVersion - Variable in class net.sf.basedb.util.Diff3

Sample - Class in net.sf.basedb.core

This class is used to represent sample items.

Sample(SampleData) - Constructor for class net.sf.basedb.core.Sample

SAMPLE - Enum constant in enum class net.sf.basedb.core.Item

The item is a Sample.

SampleData - Class in net.sf.basedb.core.data

This represents a sample.

SampleData() - Constructor for class net.sf.basedb.core.data.SampleData

SampleImporter - Class in net.sf.basedb.plugins.batchimport

Plug-in for importing sample items in a batch.

SampleImporter() - Constructor for class net.sf.basedb.plugins.batchimport.SampleImporter

SampleLoader - Class in net.sf.basedb.util.overview.loader

Node loader implementation for samples.

SampleLoader() - Constructor for class net.sf.basedb.util.overview.loader.SampleLoader

sampleQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

sampleSize - Variable in class net.sf.basedb.util.AnyToAnyLinkStatistics

SampleToBioSourceTransformer - Class in net.sf.basedb.util.listable

Source item transformer that transform sample items to their parent biosources.

SampleToBioSourceTransformer() - Constructor for class net.sf.basedb.util.listable.SampleToBioSourceTransformer

SampleToBioSourceTransformer(boolean) - Constructor for class net.sf.basedb.util.listable.SampleToBioSourceTransformer

Create a new sample to biosource transformer that only load parent biosources to sample that has a subtype with "push annotations" set.

SampleToChildSampleTransformer - Class in net.sf.basedb.util.listable

Source item transformer implementation that transform sample items to their child sample items.

SampleToChildSampleTransformer(boolean) - Constructor for class net.sf.basedb.util.listable.SampleToChildSampleTransformer

Create a new sample to child sample transformer.

SampleToChildSampleTransformer(boolean, boolean) - Constructor for class net.sf.basedb.util.listable.SampleToChildSampleTransformer

Create a new sample to child sample transformer that only load children that has a subtype with "push annotations" set.

SampleToExtractTransformer - Class in net.sf.basedb.util.listable

Source item transformer that transform sample items to their child extract.

SampleToExtractTransformer() - Constructor for class net.sf.basedb.util.listable.SampleToExtractTransformer

SampleToParentSampleTransformer - Class in net.sf.basedb.util.listable

Source item transformer implementation that transform sample items to their parent sample items.

SampleToParentSampleTransformer(boolean) - Constructor for class net.sf.basedb.util.listable.SampleToParentSampleTransformer

Create a new sample to parent sample transformer.

SampleToParentSampleTransformer(boolean, boolean) - Constructor for class net.sf.basedb.util.listable.SampleToParentSampleTransformer

Create a new sample to parent sample transformer that only load parents to samples that has a subtype with "push annotations" set.

SampleValidator - Class in net.sf.basedb.util.overview.validator

Validator implementation for sample.

SampleValidator() - Constructor for class net.sf.basedb.util.overview.validator.SampleValidator

SAMPLING - Static variable in class net.sf.basedb.core.Kit

The ID for the sampling kit type, for example a kit used when creating a Sample from a BioSource.

SAMPLING - Static variable in class net.sf.basedb.core.Protocol

The ID for the sampling protocol type, for example a protocol used when creating a Sample from a BioSource.

save() - Method in class net.sf.basedb.util.extensions.manager.Settings

Save the settings to disk.

save(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

save(String, Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

SAVE_AS - Static variable in class net.sf.basedb.core.plugin.AbstractExporterPlugin

Parameter name for the AbstractExporterPlugin.getSaveAsParameter(String, String, String, boolean) parameter.

saveAllCurrentContexts(Session, UserData, ClientData) - Method in class net.sf.basedb.core.SessionControl

saveAllUserSettings(Session) - Method in class net.sf.basedb.core.SessionControl

Saves all user settings.

saveCurrentContextAs(Item, String, boolean, boolean) - Method in class net.sf.basedb.core.SessionControl

Same as: saveCurrentContextAs(item, null, name, overwrite, isPublic).

saveCurrentContextAs(Item, String, String, boolean, boolean) - Method in class net.sf.basedb.core.SessionControl

Save the current context as a named context.

saveData(Session, BasicData) - Static method in class net.sf.basedb.core.HibernateUtil

Save a new data object to the database.

saveData(StatelessSession, BasicData) - Static method in class net.sf.basedb.core.HibernateUtil

Save a new data object to the database.

SaveIf(BasicItem, boolean) - Constructor for class net.sf.basedb.core.DbControl.SaveIf

saveIfQueue - Variable in class net.sf.basedb.core.DbControl

Lists items that are saved only if the parent item is also saved.

saveImageToFile(DbControl, BufferedImage, String, String, boolean) - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet

saveItem(BasicItem) - Method in class net.sf.basedb.core.DbControl

Schedule a new item to be saved in the database.

saveItemIf(BasicItem, BasicItem, boolean) - Method in class net.sf.basedb.core.DbControl

Schedule a new item to be saved in the database if another item is also saved.

saveOrUpdate(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

saveOrUpdate(String, Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

saveParameters(DbControl) - Method in class net.sf.basedb.core.PluginResponse

Save all parameters that has been configured during the configuration sequence to the database.

saveParameters(DbControl, GuiContext) - Method in class net.sf.basedb.core.PluginRequest

Save all parameters that have got values in this request/response session.

saveParameters(Job, Map<String, PluginParameter<?>>) - Method in class net.sf.basedb.core.ParameterValuesImpl

saveParameters(PluginConfiguration, Map<String, PluginParameter<?>>) - Method in class net.sf.basedb.core.ParameterValuesImpl

SavePointWork<R> - Class in net.sf.basedb.core.hibernate

A wrapper work that protects a parent work with a savepoint.

SavePointWork(ReturningWork<R>) - Constructor for class net.sf.basedb.core.hibernate.SavePointWork

Create a new work item.

saveSettings() - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Save the settings.

saveSettings(Session, Query<I>, Map<String, SessionControl.SettingInfo>, Class<I>, UserData, ClientData) - Method in class net.sf.basedb.core.SessionControl

Save settings when a user logs out.

saveState(Serializable) - Method in class net.sf.basedb.core.Job

Save the job state to the static cache.

saveTo - Variable in class net.sf.basedb.core.plugin.AbstractExporterPlugin

saveTo(OutputStream) - Method in class net.sf.basedb.util.excel.XlsxTableWriter

Save the workbook to the given stream.

saveToPreset(Presets.Preset) - Method in class net.sf.basedb.util.overview.ValidationOptions

Save the current settings to a preset.

saveValidationPresets(SessionControl) - Static method in class net.sf.basedb.util.overview.OverviewUtil

Save the validation option presets for the logged in user.

sc - Variable in class net.sf.basedb.clients.jobagent.Agent

sc - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper

sc - Variable in class net.sf.basedb.clients.web.servlet.RssNewsFeed

sc - Variable in class net.sf.basedb.clients.web.taglib.Page

The SessionControl object in use for this request.

sc - Variable in class net.sf.basedb.clients.web.taglib.table.Table

sc - Variable in class net.sf.basedb.core.AbstractBatcher

sc - Variable in class net.sf.basedb.core.Application.Pinger

sc - Variable in class net.sf.basedb.core.DataResultIterator

The SessionControl

sc - Variable in class net.sf.basedb.core.DbControl

sc - Variable in class net.sf.basedb.core.hibernate.ExecuteUpdateWork

sc - Variable in class net.sf.basedb.core.hibernate.ResultSetWork

sc - Variable in class net.sf.basedb.core.InternalJobQueue

The job queues session controller.

sc - Variable in class net.sf.basedb.core.Job.ProgressReporterImpl

sc - Variable in class net.sf.basedb.core.plugin.AbstractPlugin

sc - Variable in class net.sf.basedb.core.PluginRequest

sc - Variable in class net.sf.basedb.util.annotations.RunnableInheritAnnotationsManager

sc - Variable in class net.sf.basedb.util.extensions.ClientContext

scale - Variable in class net.sf.basedb.util.ChainedProgressReporter

scale - Variable in class net.sf.basedb.util.InputStreamTracker.LinearScaleFactor

scale(long) - Method in class net.sf.basedb.util.InputStreamTracker.CurvedScaleFactor

scale(long) - Method in class net.sf.basedb.util.InputStreamTracker.IdentityScaleFactor

scale(long) - Method in class net.sf.basedb.util.InputStreamTracker.LinearScaleFactor

scale(long) - Method in interface net.sf.basedb.util.InputStreamTracker.ScaleFactor

scaleFactor - Variable in class net.sf.basedb.util.InputStreamTracker

A scale factor to apply when counting bytes.

scan(DbControl, HttpServletRequest) - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

SCAN - Static variable in class net.sf.basedb.core.DerivedBioAssay

The id for the DerivedBioAssayType item representing a scanned hybridization.

scanForChanges() - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Scan the managed directories for new/updated/deleted extensions.

scanForChanges() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager

Scan the managed directories for new, updated and deleted files.

scanForInstalledFiles(File, Settings) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager

Scan the given directory and add files that are installed according to the settings.

scanForLinks(String) - Static method in class net.sf.basedb.clients.web.util.HTML

Scans a string for email addresses and URL:s and replaces them with <a href="---"> tags.

scanForLinks(String, int) - Static method in class net.sf.basedb.clients.web.util.HTML

Scans a string for email addresses and URL:s and replaces them with <a href="---"> tags.

scanForLinks(String, int, String) - Static method in class net.sf.basedb.clients.web.util.HTML

Scans a string for email addresses and URL:s and replaces them with <a href="---"> tags.

scanForLinks(String, String) - Static method in class net.sf.basedb.clients.web.util.HTML

Scans a string for email addresses and URL:s and replaces them with <a href="---"> tags.

scanForNewFiles(File) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager

Scan the given directory and add files that are new.

SCANNER - Static variable in class net.sf.basedb.core.Hardware

The id for the HardwareType object representing a scanner.

SCANNING - Static variable in class net.sf.basedb.core.Protocol

The ID for the scanning protocol type, for example a protocol used for scanning the microarray slide after an experiment.

ScatterPlot - Class in net.sf.basedb.util.plot

A simple plot utility for generating scatter plots without the need to delve deep into the JFreePlot package.

ScatterPlot(String, String) - Constructor for class net.sf.basedb.util.plot.ScatterPlot

Create a new ScatterPlot.

scHasBeenSet - Variable in class net.sf.basedb.clients.web.taglib.Page

schedule(TimerTask, long, boolean) - Method in class net.sf.basedb.util.timer.Scheduler

schedule(TimerTask, long, long, boolean) - Method in class net.sf.basedb.util.timer.Scheduler

schedule(TimerTask, Date, boolean) - Method in class net.sf.basedb.util.timer.Scheduler

schedule(TimerTask, Date, long, boolean) - Method in class net.sf.basedb.util.timer.Scheduler

scheduleAtFixedRate(TimerTask, long, long, boolean) - Method in class net.sf.basedb.util.timer.Scheduler

scheduleAtFixedRate(TimerTask, Date, long, boolean) - Method in class net.sf.basedb.util.timer.Scheduler

scheduled - Variable in class net.sf.basedb.core.data.JobData

scheduler - Static variable in class net.sf.basedb.core.Application

An interface for adding timed task to the core timer.

Scheduler - Class in net.sf.basedb.util.timer

This class is a cousin to the standard Timer class but only allows scheduling of tasks.

Scheduler(Timer, boolean) - Constructor for class net.sf.basedb.util.timer.Scheduler

Create a new scheduler object.

schema - Variable in class net.sf.basedb.core.hibernate.SchemaExistsWork

schema - Variable in class net.sf.basedb.core.hibernate.TableExistsWork

schema - Variable in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration

SCHEMA_FILE_URL - Static variable in class net.sf.basedb.util.extensions.xml.XmlLoader

The URL pointing to the extensions.xsd schema.

SchemaChange() - Constructor for class net.sf.basedb.core.Update.SchemaChange

schemaExists(String, String) - Method in class net.sf.basedb.core.ServiceSessionControl

SchemaExistsWork - Class in net.sf.basedb.core.hibernate

A work implementation that checks if a given catalog+schema exists in the database or not.

SchemaExistsWork(String, String) - Constructor for class net.sf.basedb.core.hibernate.SchemaExistsWork

Create a new work item.

schemaFileURL - Static variable in class net.sf.basedb.clients.web.extensions.ServletLoader

The URL pointing to the servlets.xsd schema.

SchemaGenerator - Class in net.sf.basedb.core.hibernate

Replaces the Hibernate SchemaExport and SchemaUpdate tools.

SchemaGenerator(Metadata, Dialect, DbEngine, SchemaGenerator.Mode, ProgressReporter) - Constructor for class net.sf.basedb.core.hibernate.SchemaGenerator

Create a new schema generator.

SchemaGenerator.CollectSqlTarget - Class in net.sf.basedb.core.hibernate

Helper class used for collecting SQL statements generated by Hibernate schema creation/update tools.

SchemaGenerator.Mode - Enum Class in net.sf.basedb.core.hibernate

The installation mode.

SchemaGenerator.SqlStatement - Class in net.sf.basedb.core.hibernate

schemaVersion - Static variable in class net.sf.basedb.core.Application

schemaVersion - Variable in class net.sf.basedb.core.data.SchemaVersionData

schemaVersion - Static variable in class net.sf.basedb.core.Install

schemaVersion - Variable in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration

SchemaVersionData - Class in net.sf.basedb.core.data

This class holds information about the current schema version of the database.

SchemaVersionData() - Constructor for class net.sf.basedb.core.data.SchemaVersionData

score - Variable in class net.sf.basedb.core.data.ReporterListScoreData

score - Variable in class net.sf.basedb.util.fuzzy.StringMatcher.FuzzyMatch

score() - Method in class net.sf.basedb.util.jep.ScoreFunction

Get the score value from the current sql result.

score(ReporterList) - Static method in class net.sf.basedb.core.query.Dynamic

scoreColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

ScoreFunction - Class in net.sf.basedb.util.jep

A JEP function class that adds a score(reporterListId) function to a JEP expression parser.

ScoreFunction(DbControl) - Constructor for class net.sf.basedb.util.jep.ScoreFunction

Create a new instance of this function.

ScoreFunction(DbControl, int) - Constructor for class net.sf.basedb.util.jep.ScoreFunction

Create a new instance of this function which can be used to dynamically evaluate expressions.

scoreIndex - Variable in class net.sf.basedb.util.jep.ScoreFunction

scoreMapper - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

scripts - Variable in class net.sf.basedb.clients.web.extensions.AbstractJspFactory

scripts - Variable in class net.sf.basedb.clients.web.extensions.JspContext

scripts - Variable in class net.sf.basedb.clients.web.taglib.Head

A comma-separated list of JavaScript filenames.

Scripts - Class in net.sf.basedb.clients.web.taglib.extensions

Tag for creating <script> tags from a JspContext.

Scripts() - Constructor for class net.sf.basedb.clients.web.taglib.extensions.Scripts

scroll() - Method in class net.sf.basedb.core.hibernate.QueryWrapper

scroll(ScrollMode) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

ScrollIterator<E> - Class in net.sf.basedb.core

This is an iterator view of the result from a query using the Hibernate ScrollableResults object.

ScrollIterator(ScrollableResults, boolean) - Constructor for class net.sf.basedb.core.ScrollIterator

searchInherited - Variable in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil

searchPrimary - Variable in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil

secondLevelCache - Variable in class net.sf.basedb.core.AnnotationBatcher

SecondPassSectionSpotsParser - Class in net.sf.basedb.util.importer.spotdata

The second pass of the 'spots' section extracts spot and extra value data.

SecondPassSectionSpotsParser(DbControl, BaseFileInfo, BioAssaySet, int) - Constructor for class net.sf.basedb.util.importer.spotdata.SecondPassSectionSpotsParser

Creates a new 'section spot' parser for the first pass.

section - Variable in class net.sf.basedb.core.data.BioPlateData

section - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter

section - Variable in class net.sf.basedb.util.parser.FlatFileParser

The regular expression for matching the fist line of a section.

Section(String) - Constructor for enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section

Section(String) - Constructor for class net.sf.basedb.util.bfs.MetadataModel.Section

Create a new section.

Section(JspContext) - Constructor for class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory.Section

SECTION - Enum constant in enum class net.sf.basedb.util.parser.FlatFileParser.LineType

The parsed line is the line starting a section, matching the regular expression specified by FlatFileParser.setSectionRegexp(Pattern).

SECTION - Static variable in class net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser

The section of the BASEfile this parser can parse, eg.

SECTION_END_EVENT - Static variable in class net.sf.basedb.util.bfs.MetadataParser

Event type that is issued at the end of each section in the file.

SECTION_EVENT - Static variable in class net.sf.basedb.util.bfs.MetadataParser

Event type that is issued for each new section that is found in the file.

SectionAction - Interface in net.sf.basedb.clients.web.extensions.section

Action that inserts a new section in a jsp page.

SectionAssaysParser - Class in net.sf.basedb.util.importer.spotdata

Parses the 'assays' section of a BASEfile with bioassay set spot data.

SectionAssaysParser(DbControl, BaseFileInfo) - Constructor for class net.sf.basedb.util.importer.spotdata.SectionAssaysParser

Creates a new 'section assays' parser.

SectionBean - Class in net.sf.basedb.clients.web.extensions.section

A simple bean-like implementation of the SectionAction interface.

SectionBean() - Constructor for class net.sf.basedb.clients.web.extensions.section.SectionBean

sectionColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter

sectionCount - Variable in class net.sf.basedb.util.basefile.BaseFileParser

sectionCount - Variable in class net.sf.basedb.util.bfs.MetadataWriter

sectionCount - Variable in class net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser

sectionCount - Variable in class net.sf.basedb.util.importer.spotdata.SecondPassSectionSpotsParser

sectionCount - Variable in class net.sf.basedb.util.importer.spotdata.SectionReporterListParser

sectionEntries - Variable in class net.sf.basedb.util.bfs.MetadataParser

SectionEntry(String, String) - Constructor for class net.sf.basedb.util.bfs.MetadataModel.SectionEntry

Create a new single-valued section entry.

SectionEntry(String, String...) - Constructor for class net.sf.basedb.util.bfs.MetadataModel.SectionEntry

Create a new section entry with an array of values.

SectionHeaders(String, String, String) - Constructor for class net.sf.basedb.clients.web.fileupload.FileUpload.SectionHeaders

sectionMapper - Variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter

sectionRegexpParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter

Parameter definition that asks for the regular expression that matches a section line and extracts the section name.

SectionReporterListParser - Class in net.sf.basedb.util.importer.spotdata

Parses the 'reporterlist' section of a BASEfile.

SectionReporterListParser(DbControl, BaseFileInfo, Transformation) - Constructor for class net.sf.basedb.util.importer.spotdata.SectionReporterListParser

sections - Variable in class net.sf.basedb.util.bfs.MetadataModel

seemsLikeAnExcelFile(File) - Static method in class net.sf.basedb.util.excel.XlsxToCsvUtil

Check the MIME type and file extension to see if the file could be an Excel file.

select - Variable in class net.sf.basedb.core.query.SelectedExpression

select(ExtraValue, String) - Static method in class net.sf.basedb.core.query.Dynamic

Select an extra value.

select(Select) - Method in class net.sf.basedb.core.AbstractEntityQuery

Not supported.

select(Select) - Method in class net.sf.basedb.core.AbstractQuery

select(Select) - Method in interface net.sf.basedb.core.query.Query

Add a selection query element to the selection list.

select(VirtualColumn) - Static method in class net.sf.basedb.core.query.Dynamic

Select a column in the root table.

select(VirtualTable, VirtualColumn) - Static method in class net.sf.basedb.core.query.Dynamic

Select a column in a joined or the root table.

Select - Class in net.sf.basedb.clients.web.taglib

This tag is used to display a selection list of items.

Select - Interface in net.sf.basedb.core.query

A selection query element.

Select() - Constructor for class net.sf.basedb.clients.web.taglib.Select

SELECT - Enum constant in enum class net.sf.basedb.core.query.QuerySection

SELECT_FILTER - Static variable in class net.sf.basedb.clients.web.ModeInfo

SELECT_JOBAGENT - Enum constant in enum class net.sf.basedb.core.Permission

This permission allows a user to specify which job agent a job should be executed on using Job.setJobAgent(JobAgent).

selectdefault - Variable in class net.sf.basedb.clients.web.taglib.Select

If the default item should be selected for new items with no current or recently used items.

selected - Variable in class net.sf.basedb.core.ItemContext

selected(Select) - Static method in class net.sf.basedb.core.query.Expressions

Create an expression for an already selected query element.

selectedColumns - Variable in class net.sf.basedb.clients.web.DynamicUtil.SelectedInfo

selectedDirs - Variable in class net.sf.basedb.plugins.PackedFileExporter

SelectedExpression - Class in net.sf.basedb.core.query

An expression representing an already selected expression.

SelectedExpression(Select) - Constructor for class net.sf.basedb.core.query.SelectedExpression

selectedFiles - Variable in class net.sf.basedb.plugins.PackedFileExporter

selectedFilesAndDirs - Variable in class net.sf.basedb.plugins.PackedFileExporter

selectedIds - Variable in class net.sf.basedb.clients.web.DynamicUtil.SelectedInfo

SelectedInfo(List<String>, List<String>, List<TableColumn>) - Constructor for class net.sf.basedb.clients.web.DynamicUtil.SelectedInfo

selectedProperties - Variable in class net.sf.basedb.clients.web.DynamicUtil.SelectedInfo

selectedSubtype - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

SELECTION_MODE - Static variable in class net.sf.basedb.clients.web.ModeInfo

selectionMode - Variable in class net.sf.basedb.clients.web.ModeInfo

SELECTMULTIPLE - Static variable in class net.sf.basedb.clients.web.ModeInfo

SELECTMULTIPLE_NOBUTTONS - Static variable in class net.sf.basedb.clients.web.ModeInfo

SELECTONE - Static variable in class net.sf.basedb.clients.web.ModeInfo

selectOrderByColumnsIfDistinct() - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine

Returns FALSE.

selectOrderByColumnsIfDistinct() - Method in interface net.sf.basedb.core.dbengine.DbEngine

If the database requires that columns appearing in the ORDER BY part of the query must also be part of the SELECT list when using the DISTINCT keyword.

selectOrderByColumnsIfDistinct() - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine

Returns TRUE.

selectPermanent(Select) - Method in class net.sf.basedb.core.AbstractEntityQuery

Not supported.

selectPermanent(Select) - Method in class net.sf.basedb.core.AbstractQuery

selectPermanent(Select) - Method in interface net.sf.basedb.core.query.Query

Permanently add a selection query element to the selection list.

selectRawBioAssay(String) - Static method in class net.sf.basedb.core.query.Dynamic

Select a column in the rawbioassay table.

selectRawData(String) - Static method in class net.sf.basedb.core.query.Dynamic

Select a column in the raw data table.

selectRecent - Variable in class net.sf.basedb.clients.web.taglib.Select

If we can select the most recently used item for new items with nu current item.

selectReporter(String) - Static method in class net.sf.basedb.core.query.Dynamic

Select a column in the reporters table.

selectReporter(String, Boolean) - Static method in class net.sf.basedb.core.query.Dynamic

Select a column in the reporters table.

selects - Variable in class net.sf.basedb.core.AbstractQuery

List of selections added to the query.

Selects - Class in net.sf.basedb.core.query

A factory class to create select expressions.

Selects() - Constructor for class net.sf.basedb.core.query.Selects

send(String) - Method in class net.sf.basedb.util.jobagent.JobAgentConnection

Send a remote control command to the job agent.

send(String, Signal) - Method in class net.sf.basedb.core.signal.LocalSignalReceiver

Send the signal to a registered handler.

send(Socket, String, boolean) - Static method in class net.sf.basedb.util.SocketUtil

Send output to a socket.

send(Signal) - Method in class net.sf.basedb.core.Job.JobSignalTransporter

send(Signal) - Method in class net.sf.basedb.core.signal.ExtensionSignalTransporter

send(Signal) - Method in class net.sf.basedb.core.signal.LocalSignalTransporter

Send the signal to a local signal receiver.

send(Signal) - Method in interface net.sf.basedb.core.signal.SignalTransporter

Send a signal.

send(Signal) - Method in class net.sf.basedb.core.signal.SocketSignalTransporter

Connect to the remote host and send the signal.

sendAsEmail - Variable in class net.sf.basedb.core.Message

sendAsEmail() - Method in class net.sf.basedb.core.Message

Send this message as an email.

sendCmd(Socket, String) - Method in class net.sf.basedb.util.jobagent.JobAgentConnection

Send a command to the job agent and return the answer.

sendEmailVerificationCode(String) - Method in class net.sf.basedb.core.User

Send a verification code to the currently registered email address.

senderEmail - Static variable in class net.sf.basedb.util.EmailUtil

senderName - Static variable in class net.sf.basedb.util.EmailUtil

sendErrorMessage(SessionControl, int, Throwable) - Method in class net.sf.basedb.core.InternalJobQueue

sendMessage - Variable in class net.sf.basedb.core.data.JobData

sendMessage() - Method in class net.sf.basedb.core.Job

Send a message to the owner of the job when the job has finished

sendMessagesAsEmail - Variable in class net.sf.basedb.core.data.UserData

sendPause() - Method in class net.sf.basedb.util.jobagent.JobAgentConnection

sendPing() - Method in class net.sf.basedb.util.jobagent.JobAgentConnection

Send the ping command to the job agent.

SendSignalRenderer(Signal) - Constructor for class net.sf.basedb.core.signal.ExtensionSignalTransporter.SendSignalRenderer

sendStart() - Method in class net.sf.basedb.util.jobagent.JobAgentConnection

Send a start request to the job agent.

sendStop() - Method in class net.sf.basedb.util.jobagent.JobAgentConnection

sendTo(SignalHandler) - Method in class net.sf.basedb.core.signal.ShutdownSignalSender

sendTo(SignalHandler) - Method in interface net.sf.basedb.core.signal.SignalSender

Send a signal to the specific signal handler.

sendTo(SignalHandler) - Method in class net.sf.basedb.core.signal.SimpleSignalSender

sendToAll(SignalSender) - Method in class net.sf.basedb.clients.web.util.SimpleSignalProgressReporter

sendToAll(SignalSender) - Method in class net.sf.basedb.core.signal.AbstractSignalReceiver

sendToAll(SignalSender) - Method in interface net.sf.basedb.core.signal.SignalReceiver

Let the signal sender send one or more signals to all registered signal handlers on this reciever.

separator - Variable in class net.sf.basedb.clients.web.taglib.path.Path

separator - Variable in class net.sf.basedb.clients.web.taglib.table.CellValue

separator - Static variable in class net.sf.basedb.core.File

separator - Variable in class net.sf.basedb.util.formatter.CollectionFormatter

SEPARATOR - Enum constant in enum class net.sf.basedb.clients.web.extensions.menu.MenuItemAction.MenuType

This is a separator line.

SequenceFilenameGenerator - Class in net.sf.basedb.util.bfs

File name generator implementation that generates file names using a simple numerical counter.

SequenceFilenameGenerator() - Constructor for class net.sf.basedb.util.bfs.SequenceFilenameGenerator

Create a new sequence file name generator.

SequenceFilenameGenerator(String, String, int) - Constructor for class net.sf.basedb.util.bfs.SequenceFilenameGenerator

Create a new sequence file name generator.

SEQUENCER - Static variable in class net.sf.basedb.core.Hardware

The id for the HardwareType object representing a sequencer.

SEQUENCES - Static variable in class net.sf.basedb.core.DerivedBioAssay

The id for the DerivedBioAssayType item representing original sequenced data.

SEQUENCING - Static variable in class net.sf.basedb.core.Kit

The ID for the sequencing kit type, for example a kit used when creating a DerivedBioAssay from a PhysicalBioAssay.

SEQUENCING - Static variable in class net.sf.basedb.core.Platform

The external id for the generic Sequencing platform.

SEQUENCING - Static variable in class net.sf.basedb.core.Protocol

The ID for the sequencing protocol type, for example a protocol used when creating a DerivedBioAssay from a PhysicalBioAssay

SEQUENCING_EXPRESSION - Static variable in class net.sf.basedb.core.PlatformVariant

The external id for the expression-like sequencing data.

SerialBaseFileExporter - Class in net.sf.basedb.util.export.spotdata

Exporter implementation that exports bioassay set data as a serial BASEfile.

SerialBaseFileExporter() - Constructor for class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter

Create a new serial BASEfile exporter.

SerialBfsExporter - Class in net.sf.basedb.util.export.spotdata

BFS exporter implementation that exports spot data in serial format.

SerialBfsExporter() - Constructor for class net.sf.basedb.util.export.spotdata.SerialBfsExporter

Create a new serial BFS exporter.

serialFormatParameter - Variable in class net.sf.basedb.plugins.Base1PluginExecuter

This parameter describes if the data should be exported in serial format or in matrix.

serializeObject(ObjectOutputStream) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

SerialSpotIntensityEventHandler - Class in net.sf.basedb.util.importer.spotdata

Event handler that extracts spot intensity information from serial BFS data files and inserts the values to a spot batcher.

SerialSpotIntensityEventHandler(SpotBatcher, PositionEventHandler, BioAssay[], int[]) - Constructor for class net.sf.basedb.util.importer.spotdata.SerialSpotIntensityEventHandler

Create a new spot instensity event handler.

serialVersionUID - Static variable in exception net.sf.basedb.clients.web.DuplicateWizardException

serialVersionUID - Static variable in exception net.sf.basedb.clients.web.fileupload.UploadAbortedException

serialVersionUID - Static variable in class net.sf.basedb.clients.web.servlet.CompileAll

serialVersionUID - Static variable in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyReportServlet

serialVersionUID - Static variable in class net.sf.basedb.clients.web.servlet.Download

serialVersionUID - Static variable in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet

serialVersionUID - Static variable in class net.sf.basedb.clients.web.servlet.ExtensionsServlet

serialVersionUID - Static variable in class net.sf.basedb.clients.web.servlet.PlotServlet

serialVersionUID - Static variable in class net.sf.basedb.clients.web.servlet.RssNewsFeed

serialVersionUID - Static variable in class net.sf.basedb.clients.web.servlet.StartStopServlet

serialVersionUID - Static variable in class net.sf.basedb.clients.web.servlet.Upload

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.Body

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.Button

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.ButtonGroup

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.CalendarButton

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.ExceptionCatcher

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.extensions.Render

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.extensions.Scripts

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.extensions.Stylesheets

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.Head

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.Help

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.HideableSection

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.Icon

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.Input

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.menu.Menuitem

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.menu.Menuseparator

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.menu.Submenu

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.Page

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.path.Path

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.path.PathElement

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.PropertyValue

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.Select

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.StylableTag

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.SubtypeSelector

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.tab.Tab

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.tab.TabControl

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Button

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Cell

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.CellValue

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.ColumnHeaders

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.ColumnSubtitles

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Data

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.ExtensionCells

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Form

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Header

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.HeaderRow

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Headers

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Hidden

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Label

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Navigator

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Panel

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.PresetSelector

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.PropertyFilter

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Row

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Rows

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Table

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Toolbar

serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.Zoom

serialVersionUID - Static variable in exception net.sf.basedb.clients.web.WebException

serialVersionUID - Static variable in exception net.sf.basedb.core.AccountExpiredException

serialVersionUID - Static variable in exception net.sf.basedb.core.AlreadyLoggedInException

serialVersionUID - Static variable in exception net.sf.basedb.core.authentication.AuthenticationException

serialVersionUID - Static variable in exception net.sf.basedb.core.authentication.InvalidPasswordException

serialVersionUID - Static variable in exception net.sf.basedb.core.authentication.LoginException

serialVersionUID - Static variable in exception net.sf.basedb.core.authentication.UnknownLoginException

serialVersionUID - Static variable in exception net.sf.basedb.core.BaseException

serialVersionUID - Static variable in exception net.sf.basedb.core.ConfigurationException

serialVersionUID - Static variable in exception net.sf.basedb.core.ConnectionClosedException

serialVersionUID - Static variable in class net.sf.basedb.core.data.AnnotationSetData

serialVersionUID - Static variable in class net.sf.basedb.core.data.ContextIndex

serialVersionUID - Static variable in class net.sf.basedb.core.data.FileTypeIndex

serialVersionUID - Static variable in class net.sf.basedb.core.data.GuiContextData

serialVersionUID - Static variable in class net.sf.basedb.core.data.keyring.GroupGroups

serialVersionUID - Static variable in class net.sf.basedb.core.data.keyring.GroupKeys

serialVersionUID - Static variable in class net.sf.basedb.core.data.keyring.GroupProjects

serialVersionUID - Static variable in class net.sf.basedb.core.data.keyring.PluginKeys

serialVersionUID - Static variable in class net.sf.basedb.core.data.keyring.ProjectKeys

serialVersionUID - Static variable in class net.sf.basedb.core.data.keyring.RoleKeys

serialVersionUID - Static variable in class net.sf.basedb.core.data.keyring.UserGroups

serialVersionUID - Static variable in class net.sf.basedb.core.data.keyring.UserKeys

serialVersionUID - Static variable in class net.sf.basedb.core.data.keyring.UserProjects

serialVersionUID - Static variable in class net.sf.basedb.core.data.keyring.UserRoles

serialVersionUID - Static variable in class net.sf.basedb.core.data.MappingCoordinate

serialVersionUID - Static variable in class net.sf.basedb.core.data.PlateCoordinate

serialVersionUID - Static variable in class net.sf.basedb.core.data.QuotaIndex

serialVersionUID - Static variable in class net.sf.basedb.core.data.ReporterListScoreData

serialVersionUID - Static variable in class net.sf.basedb.core.data.VersionedParameter

serialVersionUID - Static variable in exception net.sf.basedb.core.DatabaseException

serialVersionUID - Static variable in exception net.sf.basedb.core.DateFormatException

serialVersionUID - Static variable in exception net.sf.basedb.core.DetachedItemException

serialVersionUID - Static variable in exception net.sf.basedb.core.DeviceNotVerifiedException

serialVersionUID - Static variable in exception net.sf.basedb.core.DisallowedValueException

serialVersionUID - Static variable in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter

serialVersionUID - Static variable in class net.sf.basedb.core.hibernate.SessionWrapper

serialVersionUID - Static variable in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

serialVersionUID - Static variable in exception net.sf.basedb.core.InvalidAnnotationException

serialVersionUID - Static variable in exception net.sf.basedb.core.InvalidDataException

serialVersionUID - Static variable in exception net.sf.basedb.core.InvalidPasswordException

serialVersionUID - Static variable in exception net.sf.basedb.core.InvalidPathException

serialVersionUID - Static variable in exception net.sf.basedb.core.InvalidRelationException

serialVersionUID - Static variable in exception net.sf.basedb.core.InvalidUseOfNullException

serialVersionUID - Static variable in exception net.sf.basedb.core.ItemAlreadyExistsException

serialVersionUID - Static variable in exception net.sf.basedb.core.ItemInUseException

serialVersionUID - Static variable in exception net.sf.basedb.core.ItemModifiedException

serialVersionUID - Static variable in exception net.sf.basedb.core.ItemNotFoundException

serialVersionUID - Static variable in class net.sf.basedb.core.log.LoggingInterceptor

serialVersionUID - Static variable in exception net.sf.basedb.core.LoginException

serialVersionUID - Static variable in exception net.sf.basedb.core.NotLoggedInException

serialVersionUID - Static variable in exception net.sf.basedb.core.NumberOutOfRangeException

serialVersionUID - Static variable in exception net.sf.basedb.core.ParameterException

serialVersionUID - Static variable in exception net.sf.basedb.core.PermissionDeniedException

serialVersionUID - Static variable in exception net.sf.basedb.core.QuotaException

serialVersionUID - Static variable in exception net.sf.basedb.core.signal.SignalException

serialVersionUID - Static variable in exception net.sf.basedb.core.signal.SignalReceivedException

serialVersionUID - Static variable in exception net.sf.basedb.core.signal.UnsupportedSignalException

serialVersionUID - Static variable in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot

serialVersionUID - Static variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot

serialVersionUID - Static variable in exception net.sf.basedb.core.StringTooLongException

serialVersionUID - Static variable in class net.sf.basedb.core.UnmodifiableResultList

serialVersionUID - Static variable in exception net.sf.basedb.core.UnsavedItemException

serialVersionUID - Static variable in exception net.sf.basedb.core.UnsupportedFileFormatException

serialVersionUID - Static variable in class net.sf.basedb.util.Enumeration

serialVersionUID - Static variable in class net.sf.basedb.util.jep.FunctionSafeJep.SafeFunctionTable

serialVersionUID - Static variable in class net.sf.basedb.util.jep.FunctionSafeJep.UnknownFunction

serialVersionUID - Static variable in class net.sf.basedb.util.NameableComparator

serialVersionUID - Static variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin

serialVersionUID - Static variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset

serialVersionUID - Static variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramSeries

serialVersionUID - Static variable in class net.sf.basedb.util.ToStringComparator

server - Variable in class net.sf.basedb.clients.jobagent.Agent

server - Variable in class net.sf.basedb.core.data.JobAgentData

server - Variable in class net.sf.basedb.core.data.JobData

server - Variable in class net.sf.basedb.core.Job.ProgressReporterImpl

server - Variable in class net.sf.basedb.util.jobagent.JobAgentConnection

SERVER_NAME - Static variable in class net.sf.basedb.clients.web.taglib.Page

The name of this webserver.

serverAddress - Variable in class net.sf.basedb.clients.jobagent.Agent

serverCertificate - Variable in class net.sf.basedb.core.data.FileServerData

serverCertificate - Variable in class net.sf.basedb.util.uri.ConnectionParameters

service - Static variable in class net.sf.basedb.core.QueryExecutor

service(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.extensions.ServletWrapper

Service a request to the wrapped servlet.

service(RequestHandler) - Method in class net.sf.basedb.clients.jobagent.Agent

Start the listener service that listens for control commands such as start, stop, pause and info.

SERVICE_STARTED - Static variable in class net.sf.basedb.clients.web.extensions.service.Services

Events of this type are sent to the extensions registry whenever a service extension is started.

SERVICE_STOPPED - Static variable in class net.sf.basedb.clients.web.extensions.service.Services

Events of this type are sent to the extensions registry whenever a service extension is stopped.

ServiceControllerAction - Interface in net.sf.basedb.clients.web.extensions.service

Action for controlling services installed under the extensions system.

Services - Class in net.sf.basedb.clients.web.extensions.service

Utility class for starting and stopping services.

Services() - Constructor for class net.sf.basedb.clients.web.extensions.service.Services

ServiceSessionControl - Class in net.sf.basedb.core

A special session control implementation used for services.

ServiceSessionControl() - Constructor for class net.sf.basedb.core.ServiceSessionControl

ServiceSessionControl.FlushSessionAction - Class in net.sf.basedb.core

Flushes the given session before the transaction is committed.

ServiceSessionControl.ServicesKeyring - Class in net.sf.basedb.core

Our own keyring containing the only permission: Permission.ACT_AS_ANOTHER_USER.

ServiceSessionControl.SessionFactoryConfiguration - Class in net.sf.basedb.core

Used for creating a configuration that is the basis for building a session factory.

ServicesEventHandler - Class in net.sf.basedb.clients.web.extensions.service

Event handler for managing services when new extension are added or existing extension are updated or deleted.

ServicesEventHandler() - Constructor for class net.sf.basedb.clients.web.extensions.service.ServicesEventHandler

ServicesKeyring() - Constructor for class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring

ServicesUtil - Class in net.sf.basedb.core

Utility class for the "services" extension point.

ServicesUtil() - Constructor for class net.sf.basedb.core.ServicesUtil

SERVLET_URL - Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl

The location where extension servlets are registered.

servletClass - Variable in class net.sf.basedb.clients.web.extensions.ServletWrapper

servletContext - Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl

servletContext - Static variable in class net.sf.basedb.clients.web.extensions.skin.ImageRemapperUtil

ServletExportOutputStream - Class in net.sf.basedb.clients.web.util

An extension to the ExportOutputStream class which directs the output to the response stream of a HttpServletResponse object.

ServletExportOutputStream(HttpServletResponse) - Constructor for class net.sf.basedb.clients.web.util.ServletExportOutputStream

Create a new servlet export stream.

ServletLoader - Class in net.sf.basedb.clients.web.extensions

Loads servlet definitions from an XML file.

ServletLoader() - Constructor for class net.sf.basedb.clients.web.extensions.ServletLoader

Create a new XML loader instance.

servletName - Variable in class net.sf.basedb.clients.web.extensions.ServletWrapperKey

servletPath - Variable in class net.sf.basedb.clients.web.extensions.plot.MAPlotFactory

servletPath - Variable in class net.sf.basedb.clients.web.extensions.RequestWrapper

servlets - Variable in class net.sf.basedb.clients.web.extensions.ServletLoader

servletsPath - Variable in class net.sf.basedb.clients.web.extensions.WebClientRegisterExtensionsProcessor

ServletWrapper - Class in net.sf.basedb.clients.web.extensions

A wrapper class for servlets defined by extensions.

ServletWrapper(Class<? extends Servlet>, String) - Constructor for class net.sf.basedb.clients.web.extensions.ServletWrapper

ServletWrapperKey - Class in net.sf.basedb.clients.web.extensions

Key implementation used to identify servlets.

ServletWrapperKey(String, String) - Constructor for class net.sf.basedb.clients.web.extensions.ServletWrapperKey

Create a new key for a servlet defined in a file with the given name.

session - Variable in class net.sf.basedb.core.AuthenticationContext

session - Variable in class net.sf.basedb.core.data.ChangeHistoryData

session - Variable in class net.sf.basedb.core.DataResultIterator

The Hibernate Session that was used in the query, null if a stateless session is used.

session - Variable in class net.sf.basedb.core.hibernate.SessionWrapper

session - Variable in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

session - Static variable in class net.sf.basedb.core.Install

session - Variable in class net.sf.basedb.core.LogControl

session - Variable in class net.sf.basedb.core.MigrateRbaToDba

session - Variable in class net.sf.basedb.core.Migration

session - Variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager

session - Variable in class net.sf.basedb.core.QueryExecutor.CancelableSession

session - Variable in class net.sf.basedb.core.QueryExecutor.CancelableStatelessSession

session - Variable in class net.sf.basedb.core.QueryRuntimeFilterManager

The Hibernate session where the filters should be enabled.

session - Variable in class net.sf.basedb.core.ServiceSessionControl.FlushSessionAction

Session - Class in net.sf.basedb.core

A session represents the time between login and logout for a single user.

Session(SessionData) - Constructor for class net.sf.basedb.core.Session

SESSION - Enum constant in enum class net.sf.basedb.core.Item

The item is an Session.

Session.QueryRuntimeFilterImpl - Class in net.sf.basedb.core

A runtime filter implementation that limits a query to only return sessions for the currently logged in user unless the logged in user has generic read permission.

sessionCache - Static variable in class net.sf.basedb.core.Application

A cache of SessionControl objects.

sessionCacheTimeout - Static variable in class net.sf.basedb.core.Application

Number of minutes a SessionControl object can be unused before it is removed from the cache.

sessionCacheTimeout() - Static method in class net.sf.basedb.core.Application

Gets the maximum number of minutes before an active session is logged out.

sessionControl - Static variable in class net.sf.basedb.core.Install

SessionControl - Class in net.sf.basedb.core

This class handles user sessions.

SessionControl(String, String, boolean, String) - Constructor for class net.sf.basedb.core.SessionControl

Creates a new SessionControl object.

SessionControl(String, SessionControl, PluginDefinition, Job) - Constructor for class net.sf.basedb.core.SessionControl

Create a new session control object using another one as the template.

SessionControl.ClientInfo - Class in net.sf.basedb.core

SessionControl.LoginInfo - Class in net.sf.basedb.core

Internal class to hold information about the logged in user.

SessionControl.MainContext - Class in net.sf.basedb.core

Represents a main context for which a "current" subcontext can be assigned.

SessionControl.SettingInfo - Class in net.sf.basedb.core

Internal class to hold information about a setting

SessionControl.UnverifiedDeviceInfo - Class in net.sf.basedb.core

Class for storing temporary device information for a user that has been authenticated but before a device has been verified.

SessionControlCacheCleaner() - Constructor for class net.sf.basedb.core.Application.SessionControlCacheCleaner

SessionData - Class in net.sf.basedb.core.data

This class holds information about a session.

SessionData() - Constructor for class net.sf.basedb.core.data.SessionData

SessionFactoryConfiguration - Class in net.sf.basedb.core.hibernate

Deprecated.

In 3.8, use ServiceSessionControl.createSessionFactoryConfiguration(String, String, int, ClassLoader) instead

SessionFactoryConfiguration(String, ClassLoader) - Constructor for class net.sf.basedb.core.hibernate.SessionFactoryConfiguration

Deprecated.

Create a configuration instance.

SessionFactoryConfiguration(String, String, int, ClassLoader) - Constructor for class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration

sessionId - Variable in class net.sf.basedb.core.data.ChangeHistoryData

sessionId - Variable in class net.sf.basedb.core.log.TransactionDetails

sessionId - Variable in class net.sf.basedb.core.SessionControl.LoginInfo

The id of the SessionData.

sessions - Variable in class net.sf.basedb.core.data.ClientData

sessions - Variable in class net.sf.basedb.core.data.UserData

sessions - Variable in class net.sf.basedb.core.data.UserDeviceData

sessionSettings - Variable in class net.sf.basedb.core.SessionControl

Stores name and value of session settings.

sessionWithOptions() - Method in class net.sf.basedb.core.hibernate.SessionWrapper

SessionWrapper - Class in net.sf.basedb.core.hibernate

Wrapper around Hibernate sessions that includes a query cache.

SessionWrapper(Session) - Constructor for class net.sf.basedb.core.hibernate.SessionWrapper

Creates a new session wrapper

set(int, I) - Method in class net.sf.basedb.core.AbstractResultList

Not supported.

set(int, T) - Method in class net.sf.basedb.core.UnmodifiableResultList

Not supported.

set(Object, E) - Method in class net.sf.basedb.util.ClassLocal

Store an object and associate it with the class of the specified instance.

set(Object, Object, SessionFactoryImplementor) - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter

Set the value of the extended property.

set(T) - Method in class net.sf.basedb.core.ItemResultList.ResultListListIterator

This operation is not supported.

SET_OWNER - Enum constant in enum class net.sf.basedb.core.Permission

This permission allows a user change the owner of an item.

SET_PERMISSION - Enum constant in enum class net.sf.basedb.core.Permission

This permission allows a user change the access permission to an item.

setAbort() - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress

Request that the upload should be aborted.

setAbout(About) - Method in class net.sf.basedb.util.extensions.ExtensionBean

setAbout(About) - Method in class net.sf.basedb.util.extensions.xml.PluginInfo

setAbout(About, boolean) - Method in class net.sf.basedb.core.PluginDefinition

Update the plug-in information with the information in the about object.

setAbsolute(long, String) - Method in class net.sf.basedb.core.SimpleAbsoluteProgressReporter

Set a basic progress level.

setAbstract(String) - Method in class net.sf.basedb.core.data.ExperimentData

setAbstract(String) - Method in class net.sf.basedb.core.Experiment

Set the abstract text for the publication of this experiment.

setAction(String) - Method in class net.sf.basedb.clients.web.taglib.table.Table

setActionClass(Class<A>) - Method in class net.sf.basedb.util.extensions.ExtensionPointBean

setActionFactory(ActionFactory<? extends A>) - Method in class net.sf.basedb.util.extensions.ExtensionBean

setActive(String) - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl

setActiveProject(ProjectData) - Method in class net.sf.basedb.core.Keyring

Set the active project.

setActiveProject(Project) - Method in class net.sf.basedb.core.SessionControl

Set the active project.

setActiveProjectId(int) - Method in class net.sf.basedb.core.data.JobData

setAddress(String) - Method in class net.sf.basedb.core.authentication.ExtraUserInformation

setAddress(String) - Method in class net.sf.basedb.core.data.UserData

setAddress(String) - Method in class net.sf.basedb.core.User

Set the address for the user, or null if unknown.

setAffiliations(String) - Method in class net.sf.basedb.core.data.ExperimentData

setAffiliations(String) - Method in class net.sf.basedb.core.Experiment

Set the affiliations for this experiment.

setAllowImmediateExecution(boolean) - Method in class net.sf.basedb.core.data.PluginDefinitionData

setAllowImmediateExecution(boolean) - Method in class net.sf.basedb.core.PluginDefinition

setAllowMultiple(boolean) - Method in class net.sf.basedb.core.data.ItemSubtypeFileTypeData

setAllowMultiple(boolean) - Method in class net.sf.basedb.core.data.PlatformFileTypeData

setAllowMultiple(boolean) - Method in class net.sf.basedb.core.ItemSubtypeFileType

Allow or disallow multiple files of this file type in a file set.

setAllowMultiple(boolean) - Method in class net.sf.basedb.core.PlatformFileType

Allow or disallow multiple files of this file type in a file set.

setAllowRendererOverrider(boolean) - Method in class net.sf.basedb.util.extensions.ExtensionPointBean

setAllProjects() - Method in class net.sf.basedb.core.snapshot.SnapshotManager

Search for project-specific annotations for all projects including the default values.

setAllsubcontexts(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector

setAnalyzeAfterImport(boolean) - Method in class net.sf.basedb.core.Migration

Should we execute an analyis command after the import has been completed.

setAnnotation(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

setAnnotation(Annotation) - Method in class net.sf.basedb.core.snapshot.AnnotationFilter

Set the annotation this filter should match.

setAnnotationId(int) - Method in class net.sf.basedb.core.snapshot.AnnotationFilter

Set the annotation this filter should match.

setAnnotations(Set<AnnotationData>) - Method in class net.sf.basedb.core.data.AnnotationSetData

setAnnotations(Set<AnnotationData>) - Method in class net.sf.basedb.core.data.AnnotationTypeData

setAnnotations(Set<AnnotationLink>) - Method in class net.sf.basedb.core.data.AnnotatedData

setAnnotations(Set<AnnotationLink>) - Method in class net.sf.basedb.core.data.BioAssayData

setAnnotations(Set<AnnotationLink>) - Method in class net.sf.basedb.core.data.BioAssaySetData

setAnnotations(Set<AnnotationLink>) - Method in class net.sf.basedb.core.data.PluginDefinitionData

setAnnotations(Set<AnnotationLink>) - Method in class net.sf.basedb.core.data.ProjectData

setAnnotations(Set<AnnotationLink>) - Method in class net.sf.basedb.core.data.RootRawBioAssayData

setAnnotations(Set<AnnotationLink>) - Method in class net.sf.basedb.core.data.WellData

setAnnotationSet(AnnotationSetData) - Method in interface net.sf.basedb.core.data.AnnotatableData

Change the annotation set.

setAnnotationSet(AnnotationSetData) - Method in class net.sf.basedb.core.data.AnnotatedData

setAnnotationSet(AnnotationSetData) - Method in class net.sf.basedb.core.data.AnnotationData

setAnnotationSet(AnnotationSetData) - Method in class net.sf.basedb.core.data.BioAssayData

setAnnotationSet(AnnotationSetData) - Method in class net.sf.basedb.core.data.BioAssaySetData

setAnnotationSet(AnnotationSetData) - Method in class net.sf.basedb.core.data.PluginDefinitionData

setAnnotationSet(AnnotationSetData) - Method in class net.sf.basedb.core.data.ProjectData

setAnnotationSet(AnnotationSetData) - Method in class net.sf.basedb.core.data.RootRawBioAssayData

setAnnotationSet(AnnotationSetData) - Method in class net.sf.basedb.core.data.WellData

setAnnotationSetId(int) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink

setAnnotationType(AnnotationType) - Method in class net.sf.basedb.core.snapshot.AnnotationTypeFilter

Set the annotation type this filter should match.

setAnnotationType(AnnotationType) - Method in class net.sf.basedb.util.export.spotdata.AnnotationAssayField

Set the annotation type of the annotations that should be exported in this field.

setAnnotationType(AnnotationTypeData) - Method in class net.sf.basedb.core.data.AnnotationData

setAnnotationTypeId(int) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink

setAnnotationTypeIds(Collection<Integer>) - Method in class net.sf.basedb.clients.web.ExperimentExplorer

Update the selected annotation types.

setAnnotationTypes(Set<AnnotationTypeData>) - Method in class net.sf.basedb.core.data.AnnotationTypeCategoryData

setAppId(String) - Method in class net.sf.basedb.core.data.SchemaVersionData

setArrayBatch(ArrayBatch) - Method in class net.sf.basedb.core.ArraySlide

Set the ArrayBatch this arrayslide belongs to.

setArrayBatch(ArrayBatchData) - Method in class net.sf.basedb.core.data.ArraySlideData

setArrayBatches(Set<ArrayBatchData>) - Method in class net.sf.basedb.core.data.ArrayDesignData

setArrayDesign(ArrayDesign) - Method in class net.sf.basedb.core.ArrayBatch

Set the ArrayDesign used in this ArrayBatch.

setArrayDesign(ArrayDesign) - Method in class net.sf.basedb.core.ArrayDesignBlock

Set the ArrayDesign for this block.

setArrayDesign(ArrayDesign) - Method in class net.sf.basedb.core.RawBioAssay

Set the ArrayDesign this raw data uses.

setArrayDesign(ArrayDesignData) - Method in class net.sf.basedb.core.data.ArrayBatchData

setArrayDesign(ArrayDesignData) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData

setArrayDesign(ArrayDesignData) - Method in class net.sf.basedb.core.data.ArrayDesignPlateData

setArrayDesign(ArrayDesignData) - Method in class net.sf.basedb.core.data.RawBioAssayData

setArrayDesignBlock(ArrayDesignBlockData) - Method in class net.sf.basedb.core.data.FeatureData

setArrayDesignBlocks(Set<ArrayDesignBlockData>) - Method in class net.sf.basedb.core.data.ArrayDesignData

setArrayDesigns(Set<ArrayDesignData>) - Method in class net.sf.basedb.core.data.JobData

setArrayDesigns(Set<ArrayDesignPlateData>) - Method in class net.sf.basedb.core.data.PlateData

setArraySlide(ArraySlide) - Method in class net.sf.basedb.core.PhysicalBioAssay

Set the ArraySlide this hybridization is using.

setArraySlide(ArraySlideData) - Method in class net.sf.basedb.core.data.PhysicalBioAssayData

setArraySlides(Set<ArraySlideData>) - Method in class net.sf.basedb.core.data.ArrayBatchData

setAssayAnnotationsWriter(AnnotationWriter) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter

Set the stream were assay annotations should be written.

setAssayFields(List<String>) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo

Set the list of all assay data fields, in the order the appear in the file.

setAssays(List<Integer>) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo

Set a list with the ID:s of all assays, in the order the appearu in the data columns.

setAssaysHaveParentAssaysMapping(boolean) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo

Set a flag that indicates if the BASEfile includes a mapping from child to parent assays.

setAttribute(String, Object) - Method in class net.sf.basedb.util.extensions.ClientContext

Set an attribute of the context.

setAttribute(String, String) - Method in class net.sf.basedb.core.authentication.LoginRequest

Set an extra attribute to use for the login request.

setAttribute(String, String) - Method in class net.sf.basedb.util.extensions.AboutBean

Set an attribute for the given name.

setAttribute(String, String, Object) - Method in class net.sf.basedb.util.extensions.Registry

Set an extra attribute on a registered extension or extension point.

setAttribute(NodeAttribute<T>, T) - Method in class net.sf.basedb.util.overview.Node

Set a node attribute.

setAuthenticationMethod(String) - Method in class net.sf.basedb.core.data.SessionData

setAuthors(String) - Method in class net.sf.basedb.core.data.ExperimentData

setAuthors(String) - Method in class net.sf.basedb.core.Experiment

Set the authors of the publication for this experiment.

setAutoCloseParsers(boolean) - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter

If this option is set then all parsers are automatically closed when all data has been read to them.

setAutoCloseWriters(boolean) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter

If this option is set then all writers are automatically closed when all data has been writted to them.

setAutoCloseWriters(boolean) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter

If this option is set then all writers are automatically closed when all data has been writted to them.

setAutoCompress(boolean) - Method in class net.sf.basedb.core.data.DirectoryData

setAutoCompress(boolean) - Method in class net.sf.basedb.core.data.MimeTypeData

setAutoCompress(boolean) - Method in class net.sf.basedb.core.Directory

Set if files of should automatically be compressed when they are uploaded to this directory.

setAutoCompress(boolean) - Method in class net.sf.basedb.core.MimeType

Set if files of this MIME type should automatically be compressed when they are uploaded to BASE.

setAutoJoinType(JoinType) - Method in class net.sf.basedb.core.AbstractEntityQuery

Specify the join type of automatic joins.

setAutoJoinType(JoinType) - Method in class net.sf.basedb.core.DynamicPositionQuery

Specify the join type of automatic joins.

setAutoJoinType(JoinType) - Method in class net.sf.basedb.core.DynamicRawDataQuery

Specify the join type of automatic joins.

setAutoJoinType(JoinType) - Method in class net.sf.basedb.core.DynamicReporterQuery

Specify the join type of automatic joins.

setAutoJoinType(JoinType) - Method in class net.sf.basedb.core.DynamicSpotQuery

Specify the join type of automatic joins.

setAutoLoadChildren(boolean) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory

Set a flag that determines if the factory should create node loaders that automatically loads child nodes or not.

setAutoPermission(int) - Method in class net.sf.basedb.core.data.ProjectData

setAutoPermission(Set<Permission>) - Method in class net.sf.basedb.core.Project

Set the default permissions to use when automatically sharing new item the project when it is the active project.

setAutoReload(boolean) - Method in class net.sf.basedb.util.units.UnitCache

Specifies if a cached unit that may have been loaded by a closed DbControl should be reloaded with the current DbControl or not.

setAutoShare(boolean) - Method in class net.sf.basedb.core.data.DirectoryData

setAutoShare(boolean) - Method in class net.sf.basedb.core.Directory

Set if new files and subdirectories of should automatically be shared with the same permissions as this directory.

setAutoshow(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Cell

setAverageMethod(int) - Method in class net.sf.basedb.core.data.ExtraValueTypeData

setAverageMethod(int) - Method in class net.sf.basedb.core.data.FormulaData

setAverageMethod(int) - Method in class net.sf.basedb.core.data.ReporterClonePropertyData

setAverageMethod(Formula.AverageMethod) - Method in class net.sf.basedb.core.ExtraValueType

Set the average method of the extra value type..

setAverageMethod(Formula.AverageMethod) - Method in class net.sf.basedb.core.Formula

Set the average method of the formula.

setAverageMethod(Formula.AverageMethod) - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField

Set the average method to use when exporting averaged data.

setAverageMethod(Formula.AverageMethod) - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField

Set the average method to use when exporting averaged data.

setAverageOnReporter(boolean) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

Specify if the exported data should be averaged on reporter or not.

setAverageOnReporter(boolean) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter

setAvoiding() - Method in class net.sf.basedb.util.listable.TransformContext

Shortcut for enabling 'avoiding' and disabling 'collecting'.

setAvoiding(boolean) - Method in class net.sf.basedb.util.listable.TransformContext

Enable/disable avoiding of returning any source items that has been previously collected.

setBarcode(String) - Method in class net.sf.basedb.core.ArraySlide

Set the barcode for the slide.

setBarcode(String) - Method in class net.sf.basedb.core.BioPlate

Sets the bio plates barcode

setBarcode(String) - Method in class net.sf.basedb.core.data.ArraySlideData

setBarcode(String) - Method in class net.sf.basedb.core.data.BioPlateData

setBarcode(String) - Method in class net.sf.basedb.core.data.PlateData

setBarcode(String) - Method in class net.sf.basedb.core.Plate

Set the barcode for the plate.

setBaseStyle(CellStyle) - Method in class net.sf.basedb.util.excel.CellStyleCreator

Set a base style to use for new cells.

setBatchIndex(int) - Method in class net.sf.basedb.core.ArraySlide

Set the index of this slide in the batch.

setBatchIndex(int) - Method in class net.sf.basedb.core.data.ArraySlideData

setBatchSize(int) - Method in class net.sf.basedb.core.AbstractBatcher

setBatchSize(int) - Method in interface net.sf.basedb.core.Batcher

Sets the batch size.

setBeanClass(String) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory

Set the name of the class to use as a bean.

setBigDecimal(int, BigDecimal) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setBigDecimal(String, BigDecimal) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setBigInteger(int, BigInteger) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setBigInteger(String, BigInteger) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setBinary(int, byte[]) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setBinary(String, byte[]) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setBioAssays(Set<BioAssayData>) - Method in class net.sf.basedb.core.data.BioAssaySetData

setBioAssays(Set<BioAssayData>) - Method in class net.sf.basedb.core.data.RawBioAssayData

setBioAssaySet(BioAssaySet) - Method in class net.sf.basedb.core.BioAssay

Set the experiment.

setBioAssaySet(BioAssaySet) - Method in class net.sf.basedb.core.ExtraValue

Set the bioassayset.

setBioAssaySet(BioAssaySetData) - Method in class net.sf.basedb.core.data.BioAssayData

setBioAssaySet(BioAssaySetData) - Method in class net.sf.basedb.core.data.ExtraValueData

setBioAssaySets(Set<BioAssaySetData>) - Method in class net.sf.basedb.core.data.ExperimentData

setBioMaterial(BioMaterialData) - Method in class net.sf.basedb.core.data.BioMaterialEventSourceData

setBioMaterial(MeasuredBioMaterialData) - Method in class net.sf.basedb.core.data.BioMaterialEventData

setBioMaterial(MeasuredBioMaterialData) - Method in class net.sf.basedb.core.data.BioWellData

setBioMaterial(MeasuredBioMaterial) - Method in class net.sf.basedb.core.BioMaterialEvent

Set the biomaterial that was affected or created by this event.

setBioMaterialEvents(Set<BioMaterialEventData>) - Method in class net.sf.basedb.core.data.BioPlateEventParticipantData

setBioMaterialType(Integer) - Method in class net.sf.basedb.core.data.BioPlateTypeData

setBioMaterialType(Item) - Method in class net.sf.basedb.core.BioPlateType

Set the type of biomaterial that can be stored on plates with this type.

setBioPlate(BioPlateData) - Method in class net.sf.basedb.core.data.BioPlateEventParticipantData

setBioPlate(BioPlateData) - Method in class net.sf.basedb.core.data.BioWellData

setBioPlateEventParticipant(BioPlateEventParticipant) - Method in class net.sf.basedb.core.MeasuredBioMaterial

setBioPlateEventParticipant(BioPlateEventParticipant) - Method in class net.sf.basedb.core.PhysicalBioAssay

setBioPlateEventParticipant(BioPlateEventParticipantData) - Method in class net.sf.basedb.core.data.BioMaterialEventData

setBioPlates(Set<BioPlateData>) - Method in class net.sf.basedb.core.data.BioPlateTypeData

setBioPlateType(BioPlateType) - Method in class net.sf.basedb.core.BioPlate

setBioPlateType(BioPlateTypeData) - Method in class net.sf.basedb.core.data.BioPlateData

setBioWell(BioWell) - Method in class net.sf.basedb.core.MeasuredBioMaterial

Sets the BioWell where this biomaterial is located.

setBioWell(BioWellData) - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData

setBioWells(Map<PlateCoordinate, BioWellData>) - Method in class net.sf.basedb.core.data.BioPlateData

setBlock(Integer) - Method in class net.sf.basedb.core.data.RawData

setBlockNumber(int) - Method in class net.sf.basedb.core.ArrayDesignBlock

Set the block number of this block.

setBlockNumber(int) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData

setBlockNumber(int) - Method in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section

setBlockSizeX(int) - Method in class net.sf.basedb.core.ArrayDesignBlock

Set the number of columns in this block.

setBlockSizeX(int) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData

setBlockSizeX(Integer) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock

setBlockSizeY(int) - Method in class net.sf.basedb.core.ArrayDesignBlock

Set the number of rows in this block.

setBlockSizeY(int) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData

setBlockSizeY(Integer) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock

setBlockValue(PrintMapFlatFileImporter.MetaBlock, FlatFileParser.Line) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter

setBofMarkerRegexp(Pattern) - Method in class net.sf.basedb.util.parser.FlatFileParser

Set a regular expression that maches a beginning-of-file marker.

setBoolean(int, boolean) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setBoolean(String, boolean) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setBooleanValues(List<Boolean>) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink

setBuild(int) - Method in class net.sf.basedb.core.data.SchemaVersionData

setBulletlist(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.CellValue

setButtonclass(String) - Method in class net.sf.basedb.clients.web.taglib.Select

setButtonicon(String) - Method in class net.sf.basedb.clients.web.taglib.Select

setButtonstyle(String) - Method in class net.sf.basedb.clients.web.taglib.Select

setButtonTag(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRenderer

Set the HTML tag to use for the "button".

setButtonTag(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRendererFactory

Set the HTML tag to use for the "button".

setButtontitle(String) - Method in class net.sf.basedb.clients.web.taglib.Select

setByte(int, byte) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setByte(String, byte) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setBytes(long) - Method in class net.sf.basedb.core.data.DataCubeData

setBytes(long) - Method in class net.sf.basedb.core.data.DataCubeExtraValueData

setBytes(long) - Method in class net.sf.basedb.core.data.DataCubeFilterData

setBytes(long) - Method in class net.sf.basedb.core.data.DataCubeLayerData

setBytes(long) - Method in class net.sf.basedb.core.data.DiskUsageData

setBytes(long) - Method in class net.sf.basedb.core.data.ExperimentData

setBytes(long) - Method in class net.sf.basedb.core.data.RawBioAssayData

setBytes(long) - Method in class net.sf.basedb.core.data.ReporterCloneTemplateData

setCacheable(boolean) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setCacheable(boolean) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setCachedObject(Object, Object) - Method in class net.sf.basedb.util.overview.GenericOverview

Store an auxilliary object in the overview cache.

setCachedObject(Object, Object) - Method in interface net.sf.basedb.util.overview.OverviewContext

Store an auxilliary object in the overview cache.

setCacheMode(CacheMode) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setCacheMode(CacheMode) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setCacheMode(CacheMode) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

setCacheRegion(String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setCacheRegion(String) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setCacheResult(boolean) - Method in class net.sf.basedb.core.AbstractHqlQuery

setCacheResult(boolean) - Method in interface net.sf.basedb.core.query.HqlQuery

Specify if the query results should be cached or not.

setCalendar(int, Calendar) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setCalendar(String, Calendar) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setCalendarDate(int, Calendar) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setCalendarDate(String, Calendar) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setCategories(Set<AnnotationTypeCategoryData>) - Method in class net.sf.basedb.core.data.AnnotationTypeData

setCellClass(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

setCellClass(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

setCellStyle(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

setCellStyle(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

setChangeHistory(ChangeHistoryData) - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData

setChangeInfo(String) - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData

setChangeType(int) - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData

setChannels(int) - Method in class net.sf.basedb.core.data.FormulaData

setChannels(int) - Method in class net.sf.basedb.core.data.PlatformData

setChannels(int) - Method in class net.sf.basedb.core.data.PlatformVariantData

setChannels(int) - Method in class net.sf.basedb.core.Formula

Set the number of channels that are required to use this formula.

setChannels(int) - Method in class net.sf.basedb.core.Platform

Set the number of channels for a file-only platform.

setChannels(int) - Method in class net.sf.basedb.core.PlatformVariant

Set the number of channels for a file-only platform variant.

setCharacter(int, char) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setCharacter(String, char) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setCharacterSet(String) - Method in class net.sf.basedb.clients.web.util.ServletExportOutputStream

Calls ServletResponse.setCharacterEncoding(String)

setCharacterSet(String) - Method in class net.sf.basedb.core.data.FileData

setCharacterSet(String) - Method in class net.sf.basedb.core.File

Set the character set used in this file (for text-files only).

setCharacterSet(String) - Method in class net.sf.basedb.core.plugin.ExportOutputStream

Do nothing should be overridden by subclasses.

setCharacterSet(String) - Method in class net.sf.basedb.util.FileExportOutputStream

Calls File.setCharacterSet(String)

setCharacterSet(String) - Method in class net.sf.basedb.util.uri.UriMetadata

setCharset(Charset) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil

Set the character set to use for the text.

setChecked(boolean) - Method in class net.sf.basedb.clients.web.taglib.Input

setChild(BioAssay) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay

Set the real child bioassay object.

setChildCreationEvents(Set<BioMaterialEventSourceData>) - Method in class net.sf.basedb.core.data.BioMaterialData

setChildHasDifferentReporterPositionMapping(boolean) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo

Set a flag that indicates if the child data has a different position/reporter mapping than the parent bioassay set.

setChildId(int) - Method in class net.sf.basedb.core.data.keyring.GroupGroups

Set the id of the child group.

setChildren(Set<BioAssayData>) - Method in class net.sf.basedb.core.data.BioAssayData

setChildren(Set<DerivedBioAssayData>) - Method in class net.sf.basedb.core.data.DerivedBioAssayData

setChildren(Set<GroupData>) - Method in class net.sf.basedb.core.data.GroupData

setChildren(Set<MeasuredBioMaterialData>) - Method in class net.sf.basedb.core.data.BioMaterialData

setChildren(Set<PlateData>) - Method in class net.sf.basedb.core.data.PlateData

setChildrenLoaded() - Method in class net.sf.basedb.util.overview.Node

Sets a flag to indicate that all children has been loaded.

setCity(String) - Method in class net.sf.basedb.util.GeoLocation

setClassName(String) - Method in class net.sf.basedb.core.data.PluginDefinitionData

setClassName(String) - Method in class net.sf.basedb.core.PluginDefinition

The class name cannot be changed.

setClassName(String) - Method in class net.sf.basedb.util.extensions.xml.PluginInfo

setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo

setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean

setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory

setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory

setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean

setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean

setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory

setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

Set the class to use in all cases.

setClazz(String) - Method in class net.sf.basedb.clients.web.taglib.ExceptionCatcher

setClazz(String) - Method in class net.sf.basedb.clients.web.taglib.StylableTag

setClazz(String) - Method in class net.sf.basedb.clients.web.taglib.tab.Tab

setClazz(String) - Method in class net.sf.basedb.clients.web.taglib.table.Cell

setClazz(String) - Method in class net.sf.basedb.clients.web.taglib.table.CellValue

setClearErrors(boolean) - Method in class net.sf.basedb.util.extensions.ExtensionsInvoker

Set a flag to indicate if existing errors should be cleared before an action is rendered.

setClearState() - Method in interface net.sf.basedb.core.plugin.Response

This can be used in the configuration phase of a plug-in to clear the stored state and nextCommand information.

setClearState() - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl

setClearState() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper

setClient(Client) - Method in class net.sf.basedb.core.ClientDefaultSetting

Set the client application this setting is valid for.

setClient(Client) - Method in class net.sf.basedb.core.Help

Set the client application this setting is valid for.

setClient(Client) - Method in class net.sf.basedb.core.UserClientSetting

Set the client application this setting is valid for.

setClient(ClientData) - Method in class net.sf.basedb.core.data.ChangeHistoryData

setClient(ClientData) - Method in class net.sf.basedb.core.data.ClientDefaultSettingData

setClient(ClientData) - Method in class net.sf.basedb.core.data.ContextData

setClient(ClientData) - Method in class net.sf.basedb.core.data.ContextIndex

setClient(ClientData) - Method in class net.sf.basedb.core.data.HelpData

setClient(ClientData) - Method in class net.sf.basedb.core.data.SessionData

setClient(ClientData) - Method in class net.sf.basedb.core.data.UserClientSettingData

setClient(ClientData) - Method in class net.sf.basedb.core.data.UserDeviceData

setClientCertificate(byte[]) - Method in class net.sf.basedb.core.data.FileServerData

setClientCertificate(byte[]) - Method in class net.sf.basedb.core.FileServer

Set the client certificate that BASE should use to authenticate with the server when connecting with https.

setClientCertificate(byte[]) - Method in class net.sf.basedb.util.uri.ConnectionParameters

setClientCertificatePassword(String) - Method in class net.sf.basedb.core.data.FileServerData

setClientCertificatePassword(String) - Method in class net.sf.basedb.core.FileServer

Set the password that is needed to unlock the client certificate.

setClientCertificatePassword(String) - Method in class net.sf.basedb.util.uri.ConnectionParameters

setClientId(Integer) - Method in class net.sf.basedb.core.data.ChangeHistoryData

setClientSettings(Set<UserClientSettingData>) - Method in class net.sf.basedb.core.data.UserData

setClone(boolean) - Method in class net.sf.basedb.util.annotations.InheritSpecification

Set a flag to inherit annotations by cloning the original values.

setCollecting() - Method in class net.sf.basedb.util.listable.TransformContext

Shortcut for enabling 'collecting' and disabling 'avoiding'.

setCollecting(boolean) - Method in class net.sf.basedb.util.listable.TransformContext

Enable/disable collecting of all source items that the transformers in this context are using.

setCollectionFormatter(Formatter<Collection<? super V>>) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

setColor(String) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup

Sets the color for this annotation group.

setColor(String, Color) - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey

setColoring(ColoringData) - Method in class net.sf.basedb.core.data.ExtraValueTypeData

setColoring(ColoringData) - Method in class net.sf.basedb.core.data.FormulaData

setColorsAuto() - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary

Arranges the colors of the groups in the order they are returned by the ExperimentExplorer.AnnotationSummary.getAnnotationGroups() set.

setColspan(int) - Method in class net.sf.basedb.clients.web.taglib.table.Header

setColumn(int) - Method in class net.sf.basedb.core.data.BioWellData

setColumn(int) - Method in class net.sf.basedb.core.data.FeatureData

setColumn(int) - Method in class net.sf.basedb.core.data.MappingCoordinate

Set the location.

setColumn(int) - Method in class net.sf.basedb.core.data.PlateCoordinate

Set the location.

setColumn(int) - Method in class net.sf.basedb.core.data.WellData

setColumn(Integer) - Method in class net.sf.basedb.core.data.RawData

setColumn(String) - Method in class net.sf.basedb.clients.web.taglib.table.Cell

setColumn(String) - Method in class net.sf.basedb.core.data.ReporterClonePropertyData

setColumnContent(String, String) - Method in class net.sf.basedb.clients.web.taglib.table.Table

setColumnCount(int) - Method in class net.sf.basedb.util.bfs.DataWriter

Set the number of data columns.

setColumnFilter(String, int, String) - Method in class net.sf.basedb.clients.web.taglib.table.Table

setColumnFormatter(int, Formatter<?>) - Method in class net.sf.basedb.util.export.TableWriter

Set a data formatter for a given column.

setColumnNo(short) - Method in class net.sf.basedb.core.data.DataCubeColumnData

setColumnNo(short) - Method in class net.sf.basedb.core.DataCubeColumn

setColumns(int) - Method in class net.sf.basedb.core.data.PlateGeometryData

setColumns(int) - Method in class net.sf.basedb.core.PlateGeometry

The number of columns cannot be changed, used at object creation only.

setColumns(String) - Method in class net.sf.basedb.clients.web.taglib.table.Table

setColumns(Set<DataCubeColumnData>) - Method in class net.sf.basedb.core.data.DataCubeData

setColumnSeparator(String) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil

Set the column separator.

setComment(String) - Method in class net.sf.basedb.core.authentication.LoginRequest

Set the comment to use.

setComment(String) - Method in class net.sf.basedb.core.BioMaterialEvent

Set the comment about this event.

setComment(String) - Method in class net.sf.basedb.core.data.BioMaterialEventData

setComment(String) - Method in class net.sf.basedb.core.data.PlateEventData

setComment(String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setComment(String) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setComment(String) - Method in class net.sf.basedb.core.PlateEvent

Set the comment about this event.

setCompleted() - Method in class net.sf.basedb.util.uri.http.HttpConnectionManager.TimeoutTimer

setCompressed(boolean) - Method in class net.sf.basedb.core.data.FileData

setCompressedSize(long) - Method in class net.sf.basedb.core.data.FileData

setCondition(String) - Method in class net.sf.basedb.core.dbengine.TableInfo.IndexInfo

setConfigurations(Set<PluginConfigurationData>) - Method in class net.sf.basedb.core.data.PluginDefinitionData

setConfigurationValues(Map<VersionedParameter, ParameterValueData<?>>) - Method in class net.sf.basedb.core.data.PluginConfigurationData

setConfigured(PluginResponse) - Method in class net.sf.basedb.core.Job.ProgressReporterImpl

setConnectionManagerFactory(String) - Method in class net.sf.basedb.core.data.FileServerData

setConnectionManagerFactoryId(String) - Method in class net.sf.basedb.core.FileServer

Set the ID of the connection manager factory.

setConnectionManagerFactoryId(String) - Method in class net.sf.basedb.util.uri.ConnectionParameters

setContact(String) - Method in class net.sf.basedb.core.data.PluginDefinitionData

setContact(String) - Method in class net.sf.basedb.core.PluginDefinition

Set contact information for this plug-in.

setContact(String) - Method in class net.sf.basedb.util.extensions.AboutBean

setContent(String) - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean

setContent(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory

setContent(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean

setContentLength(long) - Method in class net.sf.basedb.clients.web.util.ServletExportOutputStream

Calls ServletResponse.setContentLength(int)

setContentLength(long) - Method in class net.sf.basedb.core.plugin.ExportOutputStream

Do nothing.

setContentLength(long) - Method in class net.sf.basedb.util.FileExportOutputStream

Ignored.

setContentstyle(String) - Method in class net.sf.basedb.clients.web.taglib.HideableSection

setContentstyle(String) - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl

setContentStyle(String) - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory

setContentStyle(String) - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean

setContext(JspContext) - Method in class net.sf.basedb.clients.web.taglib.extensions.Render

setContext(JspContext) - Method in class net.sf.basedb.clients.web.taglib.extensions.Scripts

setContext(JspContext) - Method in class net.sf.basedb.clients.web.taglib.extensions.Stylesheets

setContext(ItemContext) - Method in class net.sf.basedb.clients.web.taglib.HideableSection

setContext(ClientContext) - Method in class net.sf.basedb.core.signal.ExtensionSignalTransporter

setContextClassLoader() - Method in class net.sf.basedb.clients.web.extensions.XJspCompiler

Sets the context class loader if this JSP page is an extension JSP page and if the extensions JAR file has been modified since the last time the class loader was set.

setContextItem(Integer) - Method in class net.sf.basedb.core.data.JobData

setContexts(Map<ContextIndex, ContextData>) - Method in class net.sf.basedb.core.data.UserData

setContexts(Set<ContextData>) - Method in class net.sf.basedb.core.data.ClientData

setContextType(int) - Method in class net.sf.basedb.core.data.GuiContextData

setContextType(Integer) - Method in class net.sf.basedb.core.data.JobData

setContinue(String) - Method in interface net.sf.basedb.core.plugin.Response

This method will continue the configuration or execution of the job with a new command to the plugin.

setContinue(String) - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl

setContinue(String) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper

setContinue(String, Serializable) - Method in interface net.sf.basedb.core.plugin.Response

Can be used by an executing job to also store state information that will be restored when the job is starting up again.

setContinue(String, Serializable) - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl

setContinue(String, Serializable) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper

setCoordinateType(int) - Method in class net.sf.basedb.core.data.DataCubeExtraValueData

setCoordinateType(ExtraValue.CoordinateType) - Method in class net.sf.basedb.core.DataCubeExtraValue

Set the coordinate type.

setCopyright(String) - Method in class net.sf.basedb.core.data.PluginDefinitionData

setCopyright(String) - Method in class net.sf.basedb.core.PluginDefinition

Update copyright information about this plug-in.

setCopyright(String) - Method in class net.sf.basedb.util.extensions.AboutBean

setCopyToStdout(boolean) - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog

Enable or disable copies of log entries to standard output.

setCount(int) - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics

setCounting(boolean) - Method in class net.sf.basedb.core.AbstractQuery

Set the counting status of the query.

setCountry(String) - Method in class net.sf.basedb.util.GeoLocation

setCreated(Date) - Method in class net.sf.basedb.core.data.JobData

setCreationEvent(BioMaterialEventData) - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData

setCreationEvent(BioMaterialEventData) - Method in class net.sf.basedb.core.data.PhysicalBioAssayData

setCryptedPassword(String) - Method in class net.sf.basedb.core.data.PasswordData

Set the encrypted password.

setCubeNo(short) - Method in class net.sf.basedb.core.data.DataCubeData

setCubeNo(short) - Method in class net.sf.basedb.core.DataCube

setCubes(short) - Method in class net.sf.basedb.core.data.VirtualDbData

setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ChannelFunction

setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ExtraValueFunction

setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.FunctionSafeJep.UnknownFunction

setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.InReporterListFunction

setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.LeftFunction

setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.Log2Function

setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.MeanFunction

setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.NotInReporterListFunction

setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.PositionFunction

Can't be changed.

setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.RawChannelFunction

setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.RawFunction

setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ReporterFunction

setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ScoreFunction

setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.SimpleJepFunction

setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.ColFunction

setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.DataNoFunction

setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.DefaultItemFunction

setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.LineNoFunction

setCurrent(BasicItem) - Method in class net.sf.basedb.clients.web.taglib.Select

setCurrent(ItemSubtype) - Method in class net.sf.basedb.clients.web.taglib.SubtypeSelector

setCurrentAnyToAny(BasicItem, File, AnyToAny) - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext

Sets the current any-to-any linked file and change the parent item.

setCurrentAnyToAny(File, AnyToAny) - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext

Sets the current any-to-any linked file.

setCurrentBioWell(BioWell) - Method in class net.sf.basedb.util.overview.node.BioPlateNameGenerator

Set the current biowell object that should be used when generating names for bioplates that are reached by navigating via a biomaterial.

setCurrentClient(String) - Method in class net.sf.basedb.core.SessionControl

setCurrentDataFile(BasicItem, File, DataFileType, FileSetMember) - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext

Sets the current data file and change the parent item.

setCurrentDataFile(File, DataFileType, FileSetMember) - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext

Sets the current data file.

setCurrentEventParticipant(BioPlateEventParticipant) - Method in class net.sf.basedb.util.overview.node.BioPlateNameGenerator

Set the current bioplate event participant object that should be used when generating names for bioplates that are part of a bioplate event.

setCurrentExtension(Extension<?>) - Method in class net.sf.basedb.util.extensions.ClientContext

setCurrentExtensionPoint(ExtensionPoint<?>) - Method in class net.sf.basedb.util.extensions.ClientContext

setCurrentFile(File) - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext

Set the current file.

setCurrentFilename(String) - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress

Sets the name of the file that is currently uploading

setCurrentItem(Object) - Method in class net.sf.basedb.util.extensions.ClientContext

Set the currently active item.

setCurrentItem(Annotatable) - Method in class net.sf.basedb.core.AnnotationBatcher

Set the current item to work with from now on.

setCurrentMapper(ImageRemapper) - Static method in class net.sf.basedb.clients.web.extensions.skin.ImageRemapperUtil

Changes the current image remapper.

setCurrentSubcontext(SessionControl.MainContext, String) - Method in class net.sf.basedb.core.SessionControl

Change the currently active subcontext for the item.

setCurrentSubtype(ItemSubtype) - Method in class net.sf.basedb.util.parser.DefaultItemFunction

Set the current subtype to use when looking for default items.

setCurrentWell(BioWell) - Method in class net.sf.basedb.util.overview.node.BioWellNameGenerator

Set the well we are currently working with.

setData(String[]) - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser.SynchronizedData

setData(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.DataNoFunction

setData(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.LineNoFunction

setData(FlatFileParser.Data, Type) - Method in class net.sf.basedb.util.parser.ColFunction

setData(FlatFileParser.Data, Type) - Method in class net.sf.basedb.util.parser.JepMapper

setDataCube(DataCubeData) - Method in class net.sf.basedb.core.data.DataCubeColumnData

setDataCube(DataCubeData) - Method in class net.sf.basedb.core.data.DataCubeExtraValueData

setDataCube(DataCubeData) - Method in class net.sf.basedb.core.data.DataCubeFilterData

setDataCube(DataCubeData) - Method in class net.sf.basedb.core.data.DataCubeLayerData

setDataCube(DataCube) - Method in class net.sf.basedb.core.DataCubeColumn

Set the experiment.

setDataCube(DataCube) - Method in class net.sf.basedb.core.DataCubeExtraValue

Set the data cube.

setDataCube(DataCube) - Method in class net.sf.basedb.core.DataCubeFilter

Set the data cube.

setDataCube(DataCube) - Method in class net.sf.basedb.core.DataCubeLayer

Set the data cube.

setDataCubeColumn(DataCubeColumnData) - Method in class net.sf.basedb.core.data.BioAssayData

setDataCubeColumn(DataCubeColumn) - Method in class net.sf.basedb.core.BioAssay

setDataCubeExtraValue(DataCubeExtraValueData) - Method in class net.sf.basedb.core.data.ExtraValueData

setDataCubeExtraValue(DataCubeExtraValue) - Method in class net.sf.basedb.core.ExtraValue

setDataCubeFilter(DataCubeFilterData) - Method in class net.sf.basedb.core.data.BioAssaySetData

setDataCubeFilter(DataCubeFilter) - Method in class net.sf.basedb.core.BioAssaySet

setDataCubeLayer(DataCubeLayerData) - Method in class net.sf.basedb.core.data.BioAssaySetData

setDataCubeLayer(DataCubeLayer) - Method in class net.sf.basedb.core.BioAssaySet

setDataCubes(Set<DataCubeData>) - Method in class net.sf.basedb.core.data.VirtualDbData

setDataFile(DbControl, FileStoreEnabled, String, File) - Static method in class net.sf.basedb.core.FileStoreUtil

Set or remove a file to FileStoreEnabled item based on the file's DataFileType.

setDataFileType(DataFileTypeData) - Method in class net.sf.basedb.core.data.FileSetMemberData

setDataFileType(DataFileTypeData) - Method in class net.sf.basedb.core.data.FileTypeIndex

setDataFileType(DataFileTypeData) - Method in class net.sf.basedb.core.data.ItemSubtypeFileTypeData

setDataFileType(DataFileTypeData) - Method in class net.sf.basedb.core.data.PlatformFileTypeData

setDataFooterRegexp(Pattern) - Method in class net.sf.basedb.util.parser.FlatFileParser

Set a regular expression that can be matched against a data footer.

setDataHeaderRegexp(Pattern) - Method in class net.sf.basedb.util.parser.FlatFileParser

Set a regular expression that can be matched against the data header.

setDataSeparator(String) - Method in class net.sf.basedb.util.export.TableWriter

Change the data separator string.

setDataSplitterRegexp(Pattern) - Method in class net.sf.basedb.util.parser.FlatFileParser

Set a regular expression that is used to split a data line into columns.

setDatatype(String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

setDataWriterFactory(DataWriterFactory<?>) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter

Set the data writer factory to use for generating spot data files.

setDate(int, Date) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setDate(String, Date) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setDateFormat(String) - Method in class net.sf.basedb.util.excel.AutoFormatter

Set the data format template to use for date values (=dates with all time components at 0).

setDateFormat(SessionControl, String) - Static method in class net.sf.basedb.clients.web.formatter.FormatterSettings

Set the format string for a date formatter.

setDateFormat(Formatter<Date>) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil

Set a date formatter to use for formatting cells with date-like values.

setDateOrToday(Date) - Static method in class net.sf.basedb.core.DateUtil

Make a copy of the date.

setDateTimeFormat(SessionControl, String) - Static method in class net.sf.basedb.clients.web.formatter.FormatterSettings

Set the format string for a datetime formatter.

setDateValues(List<Date>) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink

setDbcontrol(DbControl) - Method in class net.sf.basedb.clients.web.taglib.PropertyValue

setDbControl(DbControl) - Method in class net.sf.basedb.core.AbstractBatcher

Set the DbControl that is controlling this batcher.

setDbControl(DbControl) - Method in class net.sf.basedb.core.BasicItem

Set the DbControl object that should manage this item.

setDbControl(DbControl) - Method in class net.sf.basedb.core.DiskUsageStatistics

Set the DbControl which will be used to get statisics if it is not cached.

setDbControl(DbControl) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

Set's the DbControl that should be used to get data from the database.

setDbControl(DbControl) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter

Set's the DbControl that should be used to get data from the database.

setDbControl(DbControl) - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter

Set's the DbControl that should be used to get data from the database.

setDbControl(DbControl) - Method in class net.sf.basedb.util.units.UnitCache

Set the DbControl to use for database access

setDc(DbControl) - Method in class net.sf.basedb.clients.web.taglib.SubtypeSelector

setDc(DbControl) - Method in class net.sf.basedb.clients.web.taglib.table.ExtensionCells

setDebugEnabled(boolean) - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog

Enable or disable debug-level logging.

setDefault(boolean) - Method in class net.sf.basedb.core.data.GroupData

setDefault(boolean) - Method in class net.sf.basedb.core.data.RoleData

setDefault(boolean) - Method in class net.sf.basedb.core.Group

If this group should be assigned to new users by default or not.

setDefault(boolean) - Method in class net.sf.basedb.core.Role

If this role should be assigned to new users by default or not.

setDefaultDateFormat(Formatter<Date>) - Method in class net.sf.basedb.util.parser.FlatFileParser

Set the default date format to use when creating mappers.

setDefaultErrorHandlerFactory(ErrorHandlerFactory<Action>) - Method in class net.sf.basedb.util.extensions.Registry

Set the default error handler factory.

setDefaultitem(BasicItem) - Method in class net.sf.basedb.clients.web.taglib.Select

setDefaultitems(List<? extends BasicItem>) - Method in class net.sf.basedb.clients.web.taglib.Select

setDefaultItems(ItemParameterValueData) - Method in class net.sf.basedb.core.data.ProjectData

setDefaultNumberFormat(NumberFormat) - Method in class net.sf.basedb.util.parser.FlatFileParser

Set the default number format to use when creating mappers.

setDefaultRawDataType(RawDataType) - Method in class net.sf.basedb.core.Project

Sets a raw data type to be used as default for a project.

setDefaultReadOnly(boolean) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

setDefaultSettings(Set<ClientDefaultSettingData>) - Method in class net.sf.basedb.core.data.ClientData

setDefaultSettings(Set<UserDefaultSettingData>) - Method in class net.sf.basedb.core.data.UserData

setDefaultTimestampFormat(Formatter<Date>) - Method in class net.sf.basedb.util.parser.FlatFileParser

Set the default timestamp format to use when creating mappers.

setDefaultUnit(UnitData) - Method in class net.sf.basedb.core.data.AnnotationTypeData

setDefaultUnit(Unit) - Method in class net.sf.basedb.core.AnnotationType

Set the default unit to use for this annotation type.

setDefaultValue(String) - Method in class net.sf.basedb.core.AnnotationType

Set the recommended default value for new annotation of this annotation type.

setDefaultValue(String) - Method in class net.sf.basedb.core.data.AnnotationTypeData

setDefaultValue(String) - Method in class net.sf.basedb.plugins.executor.ParameterDefinition

Set the default value for this parameter.

setDefaultValue(String) - Method in class net.sf.basedb.util.formatter.LookupFormatter

Set a default value that is returned by the LookupFormatter.format(Object) method in case no lookup has been specified for a key.

setDelayRegistration(boolean) - Method in class net.sf.basedb.util.extensions.manager.processor.IgnoreFileProcessor

Set a flag to indicate if the actual registration of the found extensions and extension points should be delayed or not.

setDelayRegistration(boolean) - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor

Set a flag to indicate if the actual registration of the found extensions and extension points should be delayed or not.

setDelegateFirst(boolean) - Method in class net.sf.basedb.util.JarClassLoader

If the class loader should delegate to the parent class loader before trying to find the class by it's own.

setDenied(boolean) - Method in class net.sf.basedb.clients.web.taglib.Select

setDenied(int) - Method in class net.sf.basedb.core.data.keyring.PluginKeys

Set the denied permissions.

setDenied(int) - Method in class net.sf.basedb.core.data.PluginPermission

setDerivedBioAssays(Set<DerivedBioAssayData>) - Method in class net.sf.basedb.core.data.ExtractData

setDerivedBioAssays(Set<DerivedBioAssayData>) - Method in class net.sf.basedb.core.data.JobData

setDerivedBioAssays(Set<DerivedBioAssayData>) - Method in class net.sf.basedb.core.data.PhysicalBioAssayData

setDescription(String) - Method in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean

setDescription(String) - Method in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory

setDescription(String) - Method in class net.sf.basedb.clients.web.extensions.startpage.StartPageBean

setDescription(String) - Method in class net.sf.basedb.core.AnyToAny

setDescription(String) - Method in class net.sf.basedb.core.authentication.ExtraUserInformation

setDescription(String) - Method in class net.sf.basedb.core.BioAssay

setDescription(String) - Method in class net.sf.basedb.core.BioAssaySet

setDescription(String) - Method in class net.sf.basedb.core.BioPlateEvent

Set the description.

setDescription(String) - Method in class net.sf.basedb.core.BioPlateEventType

setDescription(String) - Method in class net.sf.basedb.core.BioPlateType

setDescription(String) - Method in class net.sf.basedb.core.CommonItem

setDescription(String) - Method in class net.sf.basedb.core.data.AnyToAnyData

setDescription(String) - Method in class net.sf.basedb.core.data.BioAssayData

setDescription(String) - Method in class net.sf.basedb.core.data.BioAssaySetData

setDescription(String) - Method in class net.sf.basedb.core.data.BioPlateEventTypeData

setDescription(String) - Method in class net.sf.basedb.core.data.BioPlateTypeData

setDescription(String) - Method in class net.sf.basedb.core.data.CommonData

setDescription(String) - Method in class net.sf.basedb.core.data.DataFileTypeData

setDescription(String) - Method in class net.sf.basedb.core.data.ExtraValueTypeData

setDescription(String) - Method in class net.sf.basedb.core.data.GroupData

setDescription(String) - Method in class net.sf.basedb.core.data.HelpData

setDescription(String) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData

setDescription(String) - Method in class net.sf.basedb.core.data.ItemSubtypeData

setDescription(String) - Method in class net.sf.basedb.core.data.MessageData

setDescription(String) - Method in class net.sf.basedb.core.data.MimeTypeData

setDescription(String) - Method in interface net.sf.basedb.core.data.NameableData

Set the description for the item.

setDescription(String) - Method in class net.sf.basedb.core.data.NewsData

setDescription(String) - Method in class net.sf.basedb.core.data.ParameterValueData

setDescription(String) - Method in class net.sf.basedb.core.data.PlateEventTypeData

setDescription(String) - Method in class net.sf.basedb.core.data.PlateGeometryData

setDescription(String) - Method in class net.sf.basedb.core.data.PlatformData

setDescription(String) - Method in class net.sf.basedb.core.data.PlatformVariantData

setDescription(String) - Method in class net.sf.basedb.core.data.PluginDefinitionData

setDescription(String) - Method in class net.sf.basedb.core.data.PluginTypeData

setDescription(String) - Method in class net.sf.basedb.core.data.ProjectData

setDescription(String) - Method in class net.sf.basedb.core.data.QuantityData

setDescription(String) - Method in class net.sf.basedb.core.data.QuotaData

setDescription(String) - Method in class net.sf.basedb.core.data.QuotaTypeData

setDescription(String) - Method in class net.sf.basedb.core.data.ReporterClonePropertyData

setDescription(String) - Method in class net.sf.basedb.core.data.ReporterData

setDescription(String) - Method in class net.sf.basedb.core.data.ReporterTypeData

setDescription(String) - Method in class net.sf.basedb.core.data.RoleData

setDescription(String) - Method in class net.sf.basedb.core.data.RoleKeyData

setDescription(String) - Method in class net.sf.basedb.core.data.RootRawBioAssayData

setDescription(String) - Method in class net.sf.basedb.core.data.TransformationData

setDescription(String) - Method in class net.sf.basedb.core.data.UnitData

setDescription(String) - Method in class net.sf.basedb.core.data.UserData

setDescription(String) - Method in class net.sf.basedb.core.data.UserDeviceData

setDescription(String) - Method in class net.sf.basedb.core.DataFileType

setDescription(String) - Method in class net.sf.basedb.core.Directory

setDescription(String) - Method in class net.sf.basedb.core.ExtraValueType

setDescription(String) - Method in class net.sf.basedb.core.Group

setDescription(String) - Method in class net.sf.basedb.core.Help

setDescription(String) - Method in class net.sf.basedb.core.ItemSubtype

setDescription(String) - Method in class net.sf.basedb.core.Message

setDescription(String) - Method in class net.sf.basedb.core.MimeType

setDescription(String) - Method in interface net.sf.basedb.core.Nameable

Set the description for the item.

setDescription(String) - Method in class net.sf.basedb.core.News

setDescription(String) - Method in class net.sf.basedb.core.PlateEventType

setDescription(String) - Method in class net.sf.basedb.core.PlateGeometry

setDescription(String) - Method in class net.sf.basedb.core.Platform

setDescription(String) - Method in class net.sf.basedb.core.PlatformVariant

setDescription(String) - Method in class net.sf.basedb.core.PluginType

setDescription(String) - Method in class net.sf.basedb.core.Project

setDescription(String) - Method in class net.sf.basedb.core.Quantity

setDescription(String) - Method in class net.sf.basedb.core.Quota

setDescription(String) - Method in class net.sf.basedb.core.QuotaType

setDescription(String) - Method in class net.sf.basedb.core.ReporterCloneTemplate

Allow the description to be changed with RESTRICTED_WRITE permission.

setDescription(String) - Method in class net.sf.basedb.core.ReporterType

setDescription(String) - Method in class net.sf.basedb.core.Role

setDescription(String) - Method in class net.sf.basedb.core.RoleKey

setDescription(String) - Method in class net.sf.basedb.core.RootRawBioAssay

setDescription(String) - Method in class net.sf.basedb.core.SyncFilter

setDescription(String) - Method in class net.sf.basedb.core.Transformation

setDescription(String) - Method in class net.sf.basedb.core.Unit

setDescription(String) - Method in class net.sf.basedb.core.User

setDescription(String) - Method in class net.sf.basedb.core.UserDevice

setDescription(String) - Method in class net.sf.basedb.plugins.executor.ParameterDefinition

Set a description/help text for this parmeter.

setDescription(String) - Method in class net.sf.basedb.util.extensions.AboutBean

setDescription(String) - Method in class net.sf.basedb.util.extensions.ExtensionPointBean

setDescription(NameableData, String) - Static method in class net.sf.basedb.core.NameableUtil

Set the description of a NameableData object.

setDescriptor(Object) - Method in class net.sf.basedb.util.overview.Failure

Set a descriptor on this failure.

setDestinationCount(int) - Method in class net.sf.basedb.core.data.PlateMappingData

setDestinationCount(int) - Method in class net.sf.basedb.core.PlateMapping

Set the number of produced destination plates.

setDestinationGeometry(PlateGeometryData) - Method in class net.sf.basedb.core.data.PlateMappingData

setDestinationGeometry(PlateGeometry) - Method in class net.sf.basedb.core.PlateMapping

Set the destination geometry.

setDestinationIndex(int) - Method in class net.sf.basedb.core.data.PlateData

setDestroyed(boolean) - Method in class net.sf.basedb.core.ArraySlide

Set if the slide should be flagged as destroyed.

setDestroyed(boolean) - Method in class net.sf.basedb.core.BioPlate

Set the destroyed flag.

setDestroyed(boolean) - Method in class net.sf.basedb.core.data.ArraySlideData

setDestroyed(boolean) - Method in class net.sf.basedb.core.data.BioPlateData

setDestroyed(boolean) - Method in class net.sf.basedb.core.data.PlateData

setDestroyed(boolean) - Method in class net.sf.basedb.core.Plate

Set the destroyed flag.

setDetails(Map<MappingCoordinate, MappingCoordinate>) - Method in class net.sf.basedb.core.data.PlateMappingData

setDetails(Set<ChangeHistoryDetailData>) - Method in class net.sf.basedb.core.data.ChangeHistoryData

setDevice(UserDeviceData) - Method in class net.sf.basedb.core.data.SessionData

setDevices(Set<UserDeviceData>) - Method in class net.sf.basedb.core.data.ClientData

setDevices(Set<UserDeviceData>) - Method in class net.sf.basedb.core.data.UserData

setDeviceToken(String) - Method in class net.sf.basedb.core.authentication.LoginRequest

Set the deviceToken to use.

setDirection(String) - Method in class net.sf.basedb.clients.web.taglib.table.Table

setDirection(ItemContext.SortDirection) - Method in class net.sf.basedb.clients.web.taglib.table.Table

setDirectory(DirectoryData) - Method in class net.sf.basedb.core.data.ExperimentData

setDirectory(DirectoryData) - Method in class net.sf.basedb.core.data.FileData

setDirectory(Directory) - Method in class net.sf.basedb.core.Experiment

Set the directory where it is recommended that plugins store files that are related to this experiment.

setDirectory(Directory) - Method in class net.sf.basedb.core.File

Set the directory of this File item.

setDirty(int, int) - Method in class net.sf.basedb.core.log.EntityDetails

Set the dirtyness for the property with the given index.

setDisabled(boolean) - Method in class net.sf.basedb.clients.web.taglib.Button

setDisabled(boolean) - Method in class net.sf.basedb.clients.web.taglib.Select

setDisabled(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Button

setDisabled(boolean) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData

setDisabled(boolean) - Method in class net.sf.basedb.core.data.PluginConfigurationData

setDisabled(boolean) - Method in class net.sf.basedb.core.data.PluginDefinitionData

setDisabled(boolean) - Method in class net.sf.basedb.core.data.UserData

setDisabled(boolean) - Method in class net.sf.basedb.core.PluginConfiguration

Disabled or enable this plugin configuration.

setDisabled(boolean) - Method in class net.sf.basedb.core.PluginDefinition

Disabled or enable this plugin.

setDisabled(boolean) - Method in class net.sf.basedb.core.SyncFilter

Disabled/enable this filter.

setDisabled(boolean) - Method in class net.sf.basedb.core.User

Disables or enables the account.

setDisabled(boolean) - Method in class net.sf.basedb.util.extensions.xml.PluginInfo

setDisabled(boolean) - Method in class net.sf.basedb.util.overview.validator.BasicItemNodeValidatorFactory

setDisabled(boolean) - Method in interface net.sf.basedb.util.overview.validator.NodeValidatorFactory

Disable/enabled node validation programmatically.

setDisabled(boolean) - Method in class net.sf.basedb.util.StaticCache

Disable or enable the cache.

setDisabled(String) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory

Sets the disabled/enabled status of this factory.

setDisabled(String) - Method in class net.sf.basedb.util.extensions.debug.ProxyActionFactory

Sets the disabled/enabled status of this factory.

setDisabledClazz(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

Set the class to use when the menu is disabled.

setDisabledClazz(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

Set the class to use when the button is disabled.

setDisabledIcon(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

Set the icon to use when the menu is disabled.

setDisabledIcon(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

Set the icon to use when the button is disabled.

setDisabledStyle(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

Set the style to use when the menu is disabled.

setDisabledStyle(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

Set the style to use when the button is disabled.

setDisabledTitle(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

Set the title of the menu item when it is disabled.

setDisabledTitle(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

Set the title of the button when it is disabled.

setDisabledTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

Set the tooltip of the menu item when it is disabled.

setDisabledTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

Set the tooltip of the button when it is disabled.

setDisableInheritance(boolean) - Method in class net.sf.basedb.core.AnnotationType

If this flag is set, annotations of this type can't be inherited to child items.

setDisableInheritance(boolean) - Method in class net.sf.basedb.core.data.AnnotationTypeData

setDisableinproject(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector

setDisableLogOfValues(boolean) - Method in class net.sf.basedb.core.AnnotationType

If this flag is set, the change history logging will not include actual annotation values.

setDisableLogOfValues(boolean) - Method in class net.sf.basedb.core.data.AnnotationTypeData

setDisableManualMembers(boolean) - Method in class net.sf.basedb.core.data.ItemListData

setDisableManualMembers(boolean) - Method in class net.sf.basedb.core.ItemList

Disable or enable manual modification of members.

setDisableothers(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector

setDisableOverflowCheck(boolean) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

setDisableOverflowCheck(boolean) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

setDisableOverflowCheck(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Cell

setDisableownedby(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector

setDisableRawJoinOnMergedData(boolean) - Method in class net.sf.basedb.core.DynamicSpotQuery

Disable automatic and manual joining of raw data if the bioassay set contains merged data.

setDisableremoved(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector

setDisablesharedto(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector

setDisableSyncFilters(boolean) - Method in class net.sf.basedb.core.data.ItemListData

setDisableSyncFilters(boolean) - Method in class net.sf.basedb.core.ItemList

Disable or enable synchronization of members with sync filters.

setDiskUsage(DiskUsageData) - Method in class net.sf.basedb.core.data.ExperimentData

setDiskUsage(DiskUsageData) - Method in class net.sf.basedb.core.data.FileData

setDiskUsage(DiskUsageData) - Method in class net.sf.basedb.core.data.RawBioAssayData

setDisplayAsList(boolean) - Method in class net.sf.basedb.core.AnnotationType

Set if the enumeration values should be displayed as a selection list or as radio buttons/checkboxes by the client application.

setDisplayName(String) - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean

setDisplaySymbol(String) - Method in class net.sf.basedb.core.data.UnitData

setDisplaySymbol(String) - Method in class net.sf.basedb.core.Unit

Set the display symbol for this unit.

setDistinct(boolean) - Method in class net.sf.basedb.core.AbstractQuery

setDistinct(boolean) - Method in interface net.sf.basedb.core.query.Query

Specify if the query should only return distinct rows.

setDoctype(String) - Method in class net.sf.basedb.clients.web.taglib.Page

setDone(String) - Method in interface net.sf.basedb.core.plugin.Response

This will end the job execution and report it as a success.

setDone(String) - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl

setDone(String) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper

setDone(String, Job.ExecutionTime) - Method in interface net.sf.basedb.core.plugin.Response

This will end the configuration of a job and set the estimated execution time for it.

setDone(String, Job.ExecutionTime) - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl

setDone(String, Job.ExecutionTime) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper

setDouble(int, double) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setDouble(String, double) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setDoubleValues(List<Double>) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink

setDownloadImmediately(String, Job.ExecutionTime, boolean) - Method in interface net.sf.basedb.core.plugin.Response

This will end the configuration of a export job, and start to execute it for immediate download.

setDownloadImmediately(String, Job.ExecutionTime, boolean) - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl

setDownloadImmediately(String, Job.ExecutionTime, boolean) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper

setDragcolumns(Boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Table

setDropConstraintsBeforeImport(boolean) - Method in class net.sf.basedb.core.Migration

Should we drop the unique constraints and indexes before importing data?

setDropPrimaryKeyBeforeImport(boolean) - Method in class net.sf.basedb.core.Migration

Should we drop the primary key before importing data?

setDryRun(boolean) - Method in class net.sf.basedb.core.data.JobData

setDryRun(boolean) - Method in interface net.sf.basedb.core.plugin.Response

A plug-in may call this method in it's configuration phase or after it has been executed to indicate that the job should be or was executed as a dry-run job.

setDryRun(boolean) - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl

setDryRun(boolean) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper

setDynamic(Iterator<DynamicActionAttribute>) - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem

setDynamic(Iterator<DynamicActionAttribute>) - Method in class net.sf.basedb.clients.web.taglib.menu.Menuseparator

setDynamic(Iterator<DynamicActionAttribute>) - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu

setDynamicActionAttributesSource(DynamicActionAttributes) - Method in class net.sf.basedb.clients.web.extensions.DynamicActionAttributeSupport

Set the source of dynamic action attributes.

setDynamicAttribute(String, Object) - Method in class net.sf.basedb.clients.web.extensions.DynamicActionAttributeSupport

Adds a dynamic attribute to the action.

setDynamicAttribute(String, String, Object) - Method in class net.sf.basedb.clients.web.taglib.StylableTag

setDynamicAttribute(String, String, Object) - Method in class net.sf.basedb.clients.web.taglib.tab.Tab

setEmail(String) - Method in class net.sf.basedb.core.authentication.ExtraUserInformation

The email address to the user.

setEmail(String) - Method in class net.sf.basedb.core.data.PluginDefinitionData

setEmail(String) - Method in class net.sf.basedb.core.data.UserData

setEmail(String) - Method in class net.sf.basedb.core.PluginDefinition

Set the email address that can be used to contact the developer of the plug-in.

setEmail(String) - Method in class net.sf.basedb.core.User

Set the email address to the user, or null if unknown.

setEmail(String) - Method in class net.sf.basedb.util.extensions.AboutBean

setEnabled(boolean) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

setEnabled(boolean) - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean

setEnabled(boolean) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean

setEnabled(boolean) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory

setEnabled(boolean) - Method in class net.sf.basedb.clients.web.taglib.Icon

setEnabled(boolean) - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem

setEnabled(boolean) - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu

setEnabled(boolean) - Method in class net.sf.basedb.clients.web.taglib.path.PathElement

setEnabled(String) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

setEnabled(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory

setEnabledClazz(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

Set the class to use when the menu is enabled.

setEnabledClazz(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

Set the class to use when the button is enabled.

setEnabledIcon(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

Set the icon to use when the menu is enabled.

setEnabledIcon(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

Set the icon to use when the button is enabled.

setEnableDownloadLink(boolean) - Method in class net.sf.basedb.clients.web.taglib.PropertyValue

setEnabledPermission(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

Set the minimum permission that is required to make the menu item enabled.

setEnabledPermission(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

Set the minimum permission that is required to make the button enabled.

setEnabledStyle(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

Set the style to use when the menu is enabled.

setEnabledStyle(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

Set the style to use when the button is enabled.

setEnabledTitle(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

Set the title of the menu item when it is enabled.

setEnabledTitle(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

Set the title of the button when it is enabled.

setEnabledTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

Set the tooltip of the menu item when it is enabled.

setEnabledTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

Set the tooltip of the button when it is enabled.

setEnableEditLink(boolean) - Method in class net.sf.basedb.clients.web.taglib.PropertyValue

setEnablePropertyLink(boolean) - Method in class net.sf.basedb.clients.web.taglib.PropertyValue

setEncoder(EncoderDecoder) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil

Set the encoder to use for converting text values so that they do not conflict with column or row separators.

setEncoder(EncoderDecoder) - Method in class net.sf.basedb.util.export.TableWriter

Change the encoder.

setEndDate(Date) - Method in class net.sf.basedb.core.data.NewsData

setEndDate(Date) - Method in class net.sf.basedb.core.News

Set the end date and time for this item to be published.

setEnded() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults

Set the end time of the scan.

setEnded(Date) - Method in class net.sf.basedb.core.data.JobData

setEnded(PluginResponse, boolean) - Method in class net.sf.basedb.core.Job.ProgressReporterImpl

setEntity(int, Object) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper

Deprecated.

setEntity(int, Object) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setEntity(String, Object) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper

Deprecated.

setEntity(String, Object) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setEntityParameter(String, BasicItem) - Method in class net.sf.basedb.core.AbstractHqlQuery

setEntityParameter(String, BasicItem) - Method in interface net.sf.basedb.core.query.HqlQuery

Set the value of an entity parameter.

setEntryDate(Date) - Method in class net.sf.basedb.core.AnnotationType

setEntryDate(Date) - Method in class net.sf.basedb.core.AnnotationTypeCategory

setEntryDate(Date) - Method in class net.sf.basedb.core.ArrayBatch

setEntryDate(Date) - Method in class net.sf.basedb.core.ArrayDesign

setEntryDate(Date) - Method in class net.sf.basedb.core.ArraySlide

setEntryDate(Date) - Method in class net.sf.basedb.core.BioMaterialEvent

setEntryDate(Date) - Method in class net.sf.basedb.core.BioPlate

setEntryDate(Date) - Method in class net.sf.basedb.core.BioPlateEvent

setEntryDate(Date) - Method in class net.sf.basedb.core.BioSource

setEntryDate(Date) - Method in class net.sf.basedb.core.Client

setEntryDate(Date) - Method in class net.sf.basedb.core.data.AnnotationTypeCategoryData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.AnnotationTypeData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.ArrayBatchData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.ArrayDesignData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.ArraySlideData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.BioMaterialEventData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.BioPlateData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.BioPlateEventData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.BioSourceData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.ClientData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.DerivedBioAssayData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.ExperimentData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.ExtraValueTypeData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.FormulaData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.GroupData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.HardwareData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.ItemSubtypeData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.KitData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.MimeTypeData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.NewsData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.PlateData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.PlateEventData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.PlateGeometryData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.PlateMappingData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.PlateTypeData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.PluginConfigurationData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.PluginDefinitionData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.PluginTypeData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.ProjectData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.ProtocolData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.QuotaTypeData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.RawBioAssayData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.ReporterCloneTemplateData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.ReporterData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.ReporterListData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.ReporterTypeData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.RoleData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.SoftwareData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.TagData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.UserData

setEntryDate(Date) - Method in class net.sf.basedb.core.data.UserDeviceData

setEntryDate(Date) - Method in class net.sf.basedb.core.DerivedBioAssay

setEntryDate(Date) - Method in class net.sf.basedb.core.Experiment

setEntryDate(Date) - Method in class net.sf.basedb.core.ExtraValueType

setEntryDate(Date) - Method in class net.sf.basedb.core.Formula

setEntryDate(Date) - Method in class net.sf.basedb.core.Group

setEntryDate(Date) - Method in class net.sf.basedb.core.Hardware

setEntryDate(Date) - Method in class net.sf.basedb.core.ItemSubtype

setEntryDate(Date) - Method in class net.sf.basedb.core.Kit

setEntryDate(Date) - Method in class net.sf.basedb.core.MeasuredBioMaterial

setEntryDate(Date) - Method in class net.sf.basedb.core.MimeType

setEntryDate(Date) - Method in class net.sf.basedb.core.News

setEntryDate(Date) - Method in class net.sf.basedb.core.PhysicalBioAssay

setEntryDate(Date) - Method in class net.sf.basedb.core.Plate

setEntryDate(Date) - Method in class net.sf.basedb.core.PlateEvent

setEntryDate(Date) - Method in class net.sf.basedb.core.PlateGeometry

setEntryDate(Date) - Method in class net.sf.basedb.core.PlateMapping

setEntryDate(Date) - Method in class net.sf.basedb.core.PlateType

setEntryDate(Date) - Method in class net.sf.basedb.core.PluginConfiguration

setEntryDate(Date) - Method in class net.sf.basedb.core.PluginDefinition

setEntryDate(Date) - Method in class net.sf.basedb.core.PluginType

setEntryDate(Date) - Method in class net.sf.basedb.core.Project

setEntryDate(Date) - Method in class net.sf.basedb.core.Protocol

setEntryDate(Date) - Method in class net.sf.basedb.core.QuotaType

setEntryDate(Date) - Method in class net.sf.basedb.core.RawBioAssay

setEntryDate(Date) - Method in interface net.sf.basedb.core.Registered

Set the date the entry was registered in the database.

setEntryDate(Date) - Method in class net.sf.basedb.core.ReporterCloneTemplate

setEntryDate(Date) - Method in class net.sf.basedb.core.ReporterList

setEntryDate(Date) - Method in class net.sf.basedb.core.ReporterType

setEntryDate(Date) - Method in class net.sf.basedb.core.Role

setEntryDate(Date) - Method in class net.sf.basedb.core.Software

setEntryDate(Date) - Method in class net.sf.basedb.core.Tag

setEntryDate(Date) - Method in class net.sf.basedb.core.User

setEntryDate(Date) - Method in class net.sf.basedb.core.UserDevice

setEnumeration(boolean) - Method in class net.sf.basedb.core.AnnotationType

Set if this annotation type should provide a list of predefined allowed values.

setEnumeration(boolean) - Method in class net.sf.basedb.core.data.AnnotationTypeData

setEnumeration(Enumeration<String, String>) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

setEnumeration(Enumeration<String, String>) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

setEnumerationValues(ParameterValueData<?>) - Method in class net.sf.basedb.core.data.AnnotationTypeData

setError(boolean) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile

Sets the error status.

setError(A, Throwable) - Method in class net.sf.basedb.util.extensions.ExtensionContext

setError(A, Throwable) - Method in class net.sf.basedb.util.extensions.ExtensionPointContext

setError(A, Throwable) - Method in class net.sf.basedb.util.extensions.InvokationContext

Register an error for the current extension or extension point.

setError(A, Throwable) - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension

setError(A, Throwable) - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint

setError(String, Throwable) - Method in class net.sf.basedb.core.PluginResponse

Set a singe error message.

setError(String, Throwable) - Method in class net.sf.basedb.util.extensions.ActionIterator

Register an error with a message for the current action.

setError(String, List<? extends Throwable>) - Method in interface net.sf.basedb.core.plugin.Response

This will end the job execution or configuration and report it as a failure.

setError(String, List<? extends Throwable>) - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl

setError(String, List<? extends Throwable>) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper

setError(Throwable) - Method in class net.sf.basedb.core.SimpleProgressReporter

Set an error that happened while processing some action that was reported via this progress reporter.

setError(Throwable) - Method in class net.sf.basedb.util.extensions.ActionIterator

Register an error for the current action.

setErrorclazz(String) - Method in class net.sf.basedb.clients.web.taglib.table.Cell

setErrorHandlerFactory(ErrorHandlerFactory<? super A>) - Method in class net.sf.basedb.util.extensions.ExtensionPointBean

setErrorMessage(String) - Method in class net.sf.basedb.core.data.FileSetMemberData

setErrors(int) - Method in class net.sf.basedb.util.overview.Node

Set the number of errors that was found while validating this node.

setEstimatedExecutionTime(int) - Method in class net.sf.basedb.core.data.JobData

setEvaluateFormulas(boolean) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil

setEvent(BioMaterialEventData) - Method in class net.sf.basedb.core.data.BioMaterialEventSourceData

setEvent(BioPlateEventData) - Method in class net.sf.basedb.core.data.BioPlateEventParticipantData

setEventDate(Date) - Method in class net.sf.basedb.core.BioMaterialEvent

Set the date this event was done in the lab.

setEventDate(Date) - Method in class net.sf.basedb.core.BioPlate

Set the date this plate was created.

setEventDate(Date) - Method in class net.sf.basedb.core.BioPlateEvent

Set the date this event was done in the lab.

setEventDate(Date) - Method in class net.sf.basedb.core.data.BioMaterialEventData

setEventDate(Date) - Method in class net.sf.basedb.core.data.BioPlateData

setEventDate(Date) - Method in class net.sf.basedb.core.data.BioPlateEventData

setEventDate(Date) - Method in class net.sf.basedb.core.data.PlateEventData

setEventDate(Date) - Method in class net.sf.basedb.core.PlateEvent

Set the date this event was done in the lab.

setEventParticipants(Set<BioPlateEventParticipantData>) - Method in class net.sf.basedb.core.data.BioPlateData

setEvents(Map<PlateEventTypeData, PlateEventData>) - Method in class net.sf.basedb.core.data.PlateData

setEvents(Set<BioMaterialEventData>) - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData

setEvents(Set<BioPlateEventData>) - Method in class net.sf.basedb.core.data.BioPlateEventTypeData

setEventType(int) - Method in class net.sf.basedb.core.data.BioMaterialEventData

setEventType(BioPlateEventType) - Method in class net.sf.basedb.core.BioPlateEvent

setEventType(BioPlateEventTypeData) - Method in class net.sf.basedb.core.data.BioPlateEventData

setEventTypes(Set<PlateEventTypeData>) - Method in class net.sf.basedb.core.data.PlateTypeData

setExcelSheet(String) - Method in class net.sf.basedb.util.parser.FlatFileParser

Set the name of Excel worksheet to parse if the given file is an Excel file, otherwise this is ignored.

setException(Throwable) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload

Set exception information on the associated FileUploadProgress object.

setException(Throwable) - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress

Set the exception that caused the upload to fail.

setException(Throwable) - Method in class net.sf.basedb.core.ItemContext

Set the exception that is the cause for the error in ItemContext.configureQuery(DbControl, EntityQuery, boolean).

setExcludeDefaultValues(boolean) - Method in class net.sf.basedb.core.AnnotationRestriction.Options

setExecuteCommand(String) - Method in class net.sf.basedb.core.data.JobData

setExecuteImmediately(String, Job.ExecutionTime, boolean) - Method in interface net.sf.basedb.core.plugin.Response

This will end the configuration of a job, and start to execute it immediately if the plugin is permitted to do so.

setExecuteImmediately(String, Job.ExecutionTime, boolean) - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl

setExecuteImmediately(String, Job.ExecutionTime, boolean) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper

setExperiment(ExperimentData) - Method in class net.sf.basedb.core.data.BioAssaySetData

setExperiment(ExperimentData) - Method in class net.sf.basedb.core.data.JobData

setExperiment(ExperimentData) - Method in class net.sf.basedb.core.data.ReporterListData

setExperiment(ExperimentData) - Method in class net.sf.basedb.core.data.RootRawBioAssayData

setExperiment(ExperimentData) - Method in class net.sf.basedb.core.data.TransformationData

setExperiment(ExperimentData) - Method in class net.sf.basedb.core.data.VirtualDbData

setExperiment(Experiment) - Method in class net.sf.basedb.core.BioAssaySet

Set the experiment.

setExperiment(Experiment) - Method in class net.sf.basedb.core.Job

Set the experiment this job is part of.

setExperiment(Experiment) - Method in class net.sf.basedb.core.ReporterList

Set the experiment.

setExperiment(Experiment) - Method in class net.sf.basedb.core.Transformation

Set the experiment.

setExperimentalFactors(Set<AnnotationTypeData>) - Method in class net.sf.basedb.core.data.ExperimentData

setExperimentDesign(String) - Method in class net.sf.basedb.core.data.ExperimentData

setExperimentDesign(String) - Method in class net.sf.basedb.core.Experiment

Set a text describing the experimental design.

setExperiments(Set<ExperimentData>) - Method in class net.sf.basedb.core.data.AnnotationTypeData

setExperiments(Set<ExperimentData>) - Method in class net.sf.basedb.core.data.RawBioAssayData

setExperimentType(String) - Method in class net.sf.basedb.core.data.ExperimentData

setExperimentType(String) - Method in class net.sf.basedb.core.Experiment

Set a text describing the experiment type.

setExpirationDate(Date) - Method in class net.sf.basedb.core.data.KitData

setExpirationDate(Date) - Method in class net.sf.basedb.core.data.UserData

setExpirationDate(Date) - Method in class net.sf.basedb.core.Kit

Set the expiration date.

setExpirationDate(Date) - Method in class net.sf.basedb.core.User

Sets the expiration date of the account.

setExportable(boolean) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

setExportable(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

setExportable(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

setExportCompressed(boolean) - Method in class net.sf.basedb.core.Migration

Should the exporter compress the data files or leave them as is?

setExportFormatter(Formatter<?>) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

setExportFormatterClass(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

setExportproperty(String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

setExportProperty(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

setExportProperty(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

setExporttitle(String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

setExportTitle(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

setExpression(Expression) - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField

Set the expression used to select data in the query.

setExtended(String, Object) - Method in class net.sf.basedb.core.authentication.ExtraUserInformation

Set the value of an extended property.

setExtended(String, Object) - Method in interface net.sf.basedb.core.data.ExtendableData

Set the value of an extended property.

setExtended(String, Object) - Method in class net.sf.basedb.core.data.RawData

setExtended(String, Object) - Method in class net.sf.basedb.core.data.ReporterData

setExtended(String, Object) - Method in class net.sf.basedb.core.data.UserData

setExtended(String, Object) - Method in class net.sf.basedb.core.User

Sets an extended property

setExtendedProperty(boolean) - Method in class net.sf.basedb.core.data.ReporterClonePropertyData

setExtends(String) - Method in class net.sf.basedb.util.extensions.ExtensionBean

setExtension(String) - Method in class net.sf.basedb.clients.web.taglib.extensions.Scripts

setExtension(String) - Method in class net.sf.basedb.clients.web.taglib.extensions.Stylesheets

setExtension(String) - Method in class net.sf.basedb.core.data.DataFileTypeData

setExtension(String) - Method in class net.sf.basedb.core.data.MimeTypeData

setExtension(String) - Method in class net.sf.basedb.core.DataFileType

Set the most common gile extension for data file of this type.

setExtension(String) - Method in class net.sf.basedb.core.MimeType

Set the extension variable for this MimeType item.

setExtensionPointId(String) - Method in class net.sf.basedb.core.signal.ExtensionSignalTransporter

setExtensions(ExtensionsInvoker<?>) - Method in class net.sf.basedb.clients.web.taglib.extensions.Render

setExtensions(ExtensionsInvoker<ListColumnAction<I, ?>>) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

setExtensions(ExtensionsInvoker<TabAction>) - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl

setExtensionVersion(String, String) - Static method in class net.sf.basedb.clients.web.taglib.Head

Register the version for an exteniosn JAR file.

setExternalId(String) - Method in class net.sf.basedb.core.AnnotationType

Set the external id of the annotation type.

setExternalId(String) - Method in class net.sf.basedb.core.BioMaterial

Set the external id of the biomaterial.

setExternalId(String) - Method in class net.sf.basedb.core.BioPlate

Sets the external id of this bio plate

setExternalId(String) - Method in class net.sf.basedb.core.Client

Set the external id for this Client item.

setExternalId(String) - Method in class net.sf.basedb.core.data.AnnotationTypeData

setExternalId(String) - Method in class net.sf.basedb.core.data.BioMaterialData

setExternalId(String) - Method in class net.sf.basedb.core.data.BioPlateData

setExternalId(String) - Method in class net.sf.basedb.core.data.ClientData

setExternalId(String) - Method in class net.sf.basedb.core.data.DataFileTypeData

setExternalId(String) - Method in class net.sf.basedb.core.data.ExtraValueTypeData

setExternalId(String) - Method in class net.sf.basedb.core.data.FeatureData

setExternalId(String) - Method in class net.sf.basedb.core.data.HelpData

setExternalId(String) - Method in class net.sf.basedb.core.data.ItemListData

setExternalId(String) - Method in class net.sf.basedb.core.data.JobAgentData

setExternalId(String) - Method in class net.sf.basedb.core.data.JobData

setExternalId(String) - Method in class net.sf.basedb.core.data.PlatformData

setExternalId(String) - Method in class net.sf.basedb.core.data.PlatformVariantData

setExternalId(String) - Method in class net.sf.basedb.core.data.ProtocolData

setExternalId(String) - Method in class net.sf.basedb.core.data.ReporterData

setExternalId(String) - Method in class net.sf.basedb.core.data.ReporterListData

setExternalId(String) - Method in class net.sf.basedb.core.data.UserData

setExternalId(String) - Method in class net.sf.basedb.core.DataFileType

setExternalId(String) - Method in class net.sf.basedb.core.ExtraValueType

Set the external id for this Client item.

setExternalId(String) - Method in class net.sf.basedb.core.Help

Set the external id for this Help item.

setExternalId(String) - Method in class net.sf.basedb.core.ItemList

Set the external id for this list.

setExternalId(String) - Method in class net.sf.basedb.core.Job

Set the external ID.

setExternalId(String) - Method in class net.sf.basedb.core.JobAgent

Set the external id for the job agent.

setExternalId(String) - Method in class net.sf.basedb.core.Platform

setExternalId(String) - Method in class net.sf.basedb.core.PlatformVariant

setExternalId(String) - Method in class net.sf.basedb.core.Protocol

Set the external id of the protocol.

setExternalId(String) - Method in class net.sf.basedb.core.ReporterList

Set the external id for this ReporterList item.

setExternalId(String) - Method in class net.sf.basedb.core.User

Set the external id for the user account.

setExtract(ExtractData) - Method in class net.sf.basedb.core.data.DerivedBioAssayData

setExtract(Extract) - Method in class net.sf.basedb.core.DerivedBioAssay

Set the extract that is the parent of data in this bioassay.

setExtraField(FieldInfo) - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean

setExtraFileImporter(ExtraFileImporter) - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter

setExtraInformation(ExtraUserInformation) - Method in class net.sf.basedb.core.authentication.AuthenticatedUser

Set extra information about the user.

setExtraNo(short) - Method in class net.sf.basedb.core.data.DataCubeExtraValueData

setExtraNo(short) - Method in class net.sf.basedb.core.DataCubeExtraValue

setExtraValues(Map<ExtraValueTypeData, ExtraValueData>) - Method in class net.sf.basedb.core.data.BioAssaySetData

setExtraValues(Set<DataCubeExtraValueData>) - Method in class net.sf.basedb.core.data.DataCubeData

setExtraValues(Set<ExtraValueData>) - Method in class net.sf.basedb.core.data.ExtraValueTypeData

setExtraValueType(ExtraValueTypeData) - Method in class net.sf.basedb.core.data.ExtraValueData

setExtraValueType(ExtraValueType) - Method in class net.sf.basedb.core.ExtraValue

Set the extra value type.

setFailSafe(boolean) - Method in class net.sf.basedb.core.AbstractQuery

setFailSafe(boolean) - Method in interface net.sf.basedb.core.query.Query

Set this flag to ensure that the transaction used to execute the query is allowed to continue even after a failure at the SQL level of this query.

setFavicon(String) - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory

setFavicon(String) - Method in class net.sf.basedb.clients.web.taglib.Page

setFax(String) - Method in class net.sf.basedb.core.authentication.ExtraUserInformation

setFax(String) - Method in class net.sf.basedb.core.data.UserData

setFax(String) - Method in class net.sf.basedb.core.User

Set the fax number to the user, or null if unknown.

setFeature(FeatureData) - Method in class net.sf.basedb.core.data.RawData

setFeatureDiameter(int) - Method in class net.sf.basedb.core.ArrayDesignBlock

Set the expected diameter of spots on the slide.

setFeatureDiameter(int) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData

setFeatureIdentificationMethod(int) - Method in class net.sf.basedb.core.data.ArrayDesignData

setFeatures(Set<FeatureData>) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData

setFetchSize(int) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setFetchSize(int) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setFetchSize(int) - Method in class net.sf.basedb.core.Migration

Set the JDBC fetch size to use when fetching rows from the database.

setField(String) - Method in class net.sf.basedb.util.overview.extensions.ReflectValidationRuleActionFactory

setFile(FileData) - Method in interface net.sf.basedb.core.data.FileAttachableData

Attach a file to the item.

setFile(FileData) - Method in class net.sf.basedb.core.data.FileSetMemberData

setFile(FileData) - Method in class net.sf.basedb.core.data.ProtocolData

setFile(File) - Method in interface net.sf.basedb.core.FileAttachable

Attach a file to the item.

setFile(File) - Method in class net.sf.basedb.core.Protocol

setFileId(int) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay

Set the id of the child bioassay as it appears in the BASEfile.

setFilename(String) - Method in class net.sf.basedb.clients.web.util.ServletExportOutputStream

Calls HttpServletResponse.setHeader(java.lang.String, java.lang.String) with the following values: response.setHeader("Content-Disposition", "attachment;filename=<filename>"); If the filename contains unsafe characters it is URL encoded.

setFilename(String) - Method in class net.sf.basedb.core.plugin.ExportOutputStream

Do nothing.

setFilename(String) - Method in class net.sf.basedb.util.bfs.AnnotationParser

Set the file name that this parser is reading from.

setFilename(String) - Method in class net.sf.basedb.util.bfs.AnnotationWriter

Set the file name that this writer is printing to.

setFilename(String) - Method in class net.sf.basedb.util.bfs.DataParser

Set the file name that this parser is reading from.

setFilename(String) - Method in class net.sf.basedb.util.bfs.DataWriter

Set the file name that this writer is printing to.

setFilename(String) - Method in class net.sf.basedb.util.bfs.MetadataParser

Set the file name that this writer is printing to.

setFilename(String) - Method in class net.sf.basedb.util.bfs.MetadataWriter

Set the file name that this writer is printing to.

setFilename(String) - Method in class net.sf.basedb.util.FileExportOutputStream

Calls File.setName(String) unless file names should be ignored.

setFileOnly(boolean) - Method in class net.sf.basedb.core.data.PlatformData

setFileOnly(boolean) - Method in class net.sf.basedb.core.data.PlatformVariantData

setFileProperties(File) - Method in class net.sf.basedb.util.bfs.GenericBaseDataWriterFactory

Set file properties on the newly created file object.

setFiles(Set<FileData>) - Method in class net.sf.basedb.core.data.DirectoryData

setFiles(Set<FileData>) - Method in class net.sf.basedb.core.data.FileServerData

setFileServer(FileServerData) - Method in class net.sf.basedb.core.data.FileData

setFileServer(FileServer) - Method in class net.sf.basedb.core.File

Set the file server on which this external file is located.

setFileSet(FileSetData) - Method in class net.sf.basedb.core.data.ArrayDesignData

setFileSet(FileSetData) - Method in class net.sf.basedb.core.data.BioAssaySetData

setFileSet(FileSetData) - Method in class net.sf.basedb.core.data.DerivedBioAssayData

setFileSet(FileSetData) - Method in class net.sf.basedb.core.data.ExtraValueData

setFileSet(FileSetData) - Method in class net.sf.basedb.core.data.FileSetMemberData

setFileSet(FileSetData) - Method in interface net.sf.basedb.core.data.FileStoreEnabledData

Attach a file set to the item.

setFileSet(FileSetData) - Method in class net.sf.basedb.core.data.RawBioAssayData

setFileSetMembers(Set<FileSetMemberData>) - Method in class net.sf.basedb.core.data.DataFileTypeData

setFileSize(long) - Method in class net.sf.basedb.util.bfs.AnnotationParser

Set the size of the file or -1 if not known.

setFileSize(long) - Method in class net.sf.basedb.util.bfs.DataParser

Set the size of the file or -1 if not known.

setFileSize(long) - Method in class net.sf.basedb.util.bfs.MetadataParser

Set the size of the file or -1 if not known.

setFileType(ItemSubtypeData) - Method in class net.sf.basedb.core.data.MimeTypeData

setFileType(ItemSubtype) - Method in class net.sf.basedb.core.MimeType

Set the filetype of this item.

setFileTypes(Map<DataFileTypeData, ItemSubtypeFileTypeData>) - Method in class net.sf.basedb.core.data.ItemSubtypeData

setFileTypes(Map<FileTypeIndex, PlatformFileTypeData>) - Method in class net.sf.basedb.core.data.PlatformData

setFileTypes(Set<PlatformFileTypeData>) - Method in class net.sf.basedb.core.data.PlatformVariantData

setFilltext(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Menu

setFilter(Filter<Element>) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader

Set a filter that all <extension-point>, <extension>, <ref> and <plugin-definition> tags must pass to be loaded and registered.

setFilterable(boolean) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

setFilterable(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

setFilterable(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

setFilterclass(String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

setFilterClass(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

setFilterGroup(String) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData

setFilterGroup(String) - Method in class net.sf.basedb.core.SyncFilter

Set the group that this synchronization filter belongs to.

setFilterNo(short) - Method in class net.sf.basedb.core.data.DataCubeFilterData

setFilterNo(short) - Method in class net.sf.basedb.core.DataCubeFilter

setFilterproperty(String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

setFilterProperty(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

setFilterProperty(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

setFilterrows(int) - Method in class net.sf.basedb.clients.web.taglib.table.Table

setFilters(Set<DataCubeFilterData>) - Method in class net.sf.basedb.core.data.DataCubeData

setFiltertext(String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

setFilterText(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

setFingerprintType(String) - Method in class net.sf.basedb.core.data.FileServerData

setFirstAssayFieldIndex(int) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo

Set the index of the first data column that contains assay data.

setFirstResult(int) - Method in class net.sf.basedb.core.AbstractQuery

setFirstResult(int) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setFirstResult(int) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setFirstResult(int) - Method in interface net.sf.basedb.core.query.Query

Specify that the query should start returning rows from the specified row number. 0 = start returning from the first row.

setFloat(int, float) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setFloat(String, float) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setFloatValues(List<Float>) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink

setFlushMode(FlushModeType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setFlushMode(FlushModeType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setFlushMode(FlushModeType) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

setFlushMode(FlushMode) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setFlushMode(FlushMode) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setFlushMode(FlushMode) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

Deprecated.

setForceStop(boolean) - Method in class net.sf.basedb.core.signal.ThreadSignalHandler

Deprecated.

In 3.14. Calling this is ignored and the signal handler will always use the interrupt method.

setForceUpdate(boolean) - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor

Set a flag to indicate if already registered extensions should be re-registered or not.

setFormatter(Formatter<?>) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

setFormatter(Formatter<?>) - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn

setFormatter(Formatter<?>) - Method in class net.sf.basedb.util.export.spotdata.AnnotationAssayField

Set a formatter to use for formatting the exported values.

setFormatter(Formatter<?>) - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField

Set a formatter to use for formatting the exported values.

setFormatter(Formatter<?>) - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField

Set a formatter to use for formatting the exported values.

setFormatter(Formatter<?>) - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField

Set a formatter to use for formatting the exported values.

setFormatter(Formatter<? super V>) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

setFormatterClass(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

setFormulas(List<String>) - Method in class net.sf.basedb.core.data.FormulaData

setFormulas(List<String>) - Method in class net.sf.basedb.core.Formula

Set the expressions used by this formula.

setFormulaType(Formula.Type) - Method in class net.sf.basedb.core.Formula

Set the type of the formula.

setFreeWells(int) - Method in class net.sf.basedb.core.data.BioPlateData

setFreezer(HardwareData) - Method in class net.sf.basedb.core.data.BioPlateData

setFreezer(Hardware) - Method in class net.sf.basedb.core.BioPlate

Sets the freezer where this bio plate is stored

setFrom(String) - Method in class net.sf.basedb.core.data.MessageData

setFrom(String) - Method in class net.sf.basedb.core.Message

Set the name of the sender of the message.

setFrom(BasicItem) - Method in class net.sf.basedb.core.AnyToAny

setFromId(int) - Method in class net.sf.basedb.core.data.AnyToAnyData

setFromId(int) - Method in class net.sf.basedb.core.data.MessageData

setFromType(int) - Method in class net.sf.basedb.core.data.AnyToAnyData

setGenericDataFile(DbControl, FileStoreEnabled, String, String, File) - Static method in class net.sf.basedb.core.FileStoreUtil

Set or remove a file to FileStoreEnabled item based on the file's generic ItemSubtype.

setGenericType(ItemSubtypeData) - Method in class net.sf.basedb.core.data.DataFileTypeData

setGenericType(ItemSubtype) - Method in class net.sf.basedb.core.DataFileType

Set the generic file type of this item.

setGranted(int) - Method in class net.sf.basedb.core.data.keyring.PluginKeys

Set the granted permissions.

setGranted(int) - Method in class net.sf.basedb.core.data.PluginPermission

setGroup(GroupData) - Method in class net.sf.basedb.core.data.DiskUsageData

setGroupId(int) - Method in class net.sf.basedb.core.data.keyring.GroupKeys

Set the id of the group.

setGroupId(int) - Method in class net.sf.basedb.core.data.keyring.GroupProjects

Set the id of the group.

setGroupId(int) - Method in class net.sf.basedb.core.data.keyring.UserGroups

Set the id of the group.

setGroups(Map<GroupData, Integer>) - Method in class net.sf.basedb.core.data.ItemKeyData

setGroups(Map<GroupData, Integer>) - Method in class net.sf.basedb.core.data.ProjectData

setGroups(Set<GroupData>) - Method in class net.sf.basedb.core.data.UserData

setGuiContexts(Set<GuiContextData>) - Method in class net.sf.basedb.core.data.PluginDefinitionData

setGuiContexts(Set<GuiContext>) - Method in class net.sf.basedb.core.PluginDefinition

Set the contexts where this plugin can be used.

setHardware(HardwareData) - Method in class net.sf.basedb.core.data.BioMaterialEventData

setHardware(HardwareData) - Method in class net.sf.basedb.core.data.BioPlateEventData

setHardware(HardwareData) - Method in class net.sf.basedb.core.data.DerivedBioAssayData

setHardware(HardwareData) - Method in class net.sf.basedb.core.data.PlateEventData

setHardware(Hardware) - Method in class net.sf.basedb.core.BioMaterialEvent

Get the Hardware that was used in this event.

setHardware(Hardware) - Method in class net.sf.basedb.core.BioPlateEvent

Set the Hardware that was used in this event.

setHardware(Hardware) - Method in class net.sf.basedb.core.DerivedBioAssay

Set the Hardware that was used when creating this bioassay set.

setHardware(Hardware) - Method in class net.sf.basedb.core.PlateEvent

Set the Hardware that was used in this event.

setHasData(boolean) - Method in class net.sf.basedb.core.data.RawBioAssayData

setHasFeatures(boolean) - Method in class net.sf.basedb.core.data.ArrayDesignData

setHasHiddenCharacters(boolean) - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo

setHeader(String, String) - Method in class net.sf.basedb.core.RawBioAssay

Set the value for a raw data header.

setHeader(RawBioAssay, String, String) - Method in class net.sf.basedb.util.affymetrix.CelValidator

setHeaderRegexp(Pattern) - Method in class net.sf.basedb.util.parser.FlatFileParser

Set a regular expression that can be matched against a header.

setHeaders(String...) - Method in class net.sf.basedb.util.bfs.AnnotationModel

Set the column headers.

setHeaders(Map<String, String>) - Method in class net.sf.basedb.core.data.RawBioAssayData

setHeight(int) - Method in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean

setHeight(int) - Method in class net.sf.basedb.core.AnnotationType

Set the recommended height in characters a client application should use to render an input field for annotations of this annotation type.

setHeight(int) - Method in class net.sf.basedb.core.data.AnnotationTypeData

setHeight(String) - Method in class net.sf.basedb.clients.web.extensions.plot.MAPlotFactory

setHelp(String) - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean

setHelpid(String) - Method in class net.sf.basedb.clients.web.taglib.Help

setHelpid(String) - Method in class net.sf.basedb.clients.web.taglib.tab.Tab

setHelpId(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory

setHelpId(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory

setHelpId(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean

setHelpTexts(Set<HelpData>) - Method in class net.sf.basedb.core.data.ClientData

setHibernateFlushMode(FlushMode) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setHibernateFlushMode(FlushMode) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setHibernateFlushMode(FlushMode) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

setHiddenMembers(boolean) - Method in class net.sf.basedb.core.data.GroupData

setHiddenMembers(boolean) - Method in class net.sf.basedb.core.Group

Set the hidden members flag for this group.

setHideclazz(String) - Method in class net.sf.basedb.clients.web.taglib.HideableSection

setHideClazz(String) - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory

setHideClazz(String) - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean

setHighlight(String) - Method in class net.sf.basedb.clients.web.taglib.table.Row

setHightligh(String) - Method in class net.sf.basedb.clients.web.taglib.table.Row

Deprecated.

In 3.18 due to type in the method name

setHint(String, Object) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setHint(String, Object) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setHome(String) - Method in class net.sf.basedb.util.extensions.xml.PathConverter

Set the value of the home path.

setHomeDirectory(DirectoryData) - Method in class net.sf.basedb.core.data.UserData

setHomeDirectory(Directory) - Method in class net.sf.basedb.core.User

Set the home directory for the user.

setHost(String) - Method in class net.sf.basedb.core.data.FileServerData

setHost(String) - Method in class net.sf.basedb.core.FileServer

Set the host:port that should overrride the host:port specified in file urls.

setHost(String) - Method in class net.sf.basedb.util.uri.ConnectionParameters

setHref(String) - Method in class net.sf.basedb.clients.web.taglib.Icon

setHref(String) - Method in class net.sf.basedb.clients.web.taglib.path.PathElement

setIcon(String) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

setIcon(String) - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean

setIcon(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

Set the icon to use in all cases.

setIcon(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean

setIcon(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory

setIcon(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

Set the icon to use in all cases.

setIcon(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem

setIcon(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu

setId(int) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink

setId(int) - Method in class net.sf.basedb.core.data.BasicData

Set the id of the item.

setId(int) - Method in class net.sf.basedb.core.ItemContext

Set the ID of the current item in this context.

setId(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

setId(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

setId(String) - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean

setId(String) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

setId(String) - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean

setId(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

setId(String) - Method in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean

setId(String) - Method in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean

setId(String) - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory

setId(String) - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean

setId(String) - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory

setId(String) - Method in class net.sf.basedb.clients.web.extensions.startpage.StartPageBean

setId(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory

setId(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory

setId(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean

setId(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean

setId(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory

setId(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

Set the ID of the button.

setId(String) - Method in class net.sf.basedb.util.extensions.ExtensionBean

setId(String) - Method in class net.sf.basedb.util.extensions.ExtensionPointBean

setIdentifier(boolean) - Method in class net.sf.basedb.core.AnnotationType

setIdentifier(boolean) - Method in class net.sf.basedb.core.data.AnnotationTypeData

setIdentifierOnNewItem(DbControl, I, String) - Method in class net.sf.basedb.plugins.batchimport.AnnotationIdMethod

Set the annotation on a newly created item.

setIdentifierOnNewItem(DbControl, I, String) - Method in interface net.sf.basedb.plugins.batchimport.IdMethod

Set the ID on a newly created item when this is not done by other regular column mappers.

setIgnoredFile(File, boolean) - Method in class net.sf.basedb.util.extensions.manager.Settings

Mark the given file as ignored/not ignored by the extension system.

setIgnoreNonExistingColumns(boolean) - Method in class net.sf.basedb.util.parser.ColFunction

Set to TRUE to ignore non-existing columns.

setIgnoreNonExistingColumns(boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser

Specify if trying to create a mapper with one of the FlatFileParser.getMapper(String) methods for an expression which references a non-existing column should result in an exception or be ignored.

setIgnoreRegexp(Pattern) - Method in class net.sf.basedb.util.parser.FlatFileParser

Set a regular expression that is used to match a line that should be ignored.

setIgnoreSubtypeFilter(boolean) - Method in class net.sf.basedb.core.ItemContext

Set a flag to indicate if the configured subtype should be ignored when configuring a query.

setImage(String) - Method in class net.sf.basedb.clients.web.taglib.Button

setImage(String) - Method in class net.sf.basedb.clients.web.taglib.Help

setImage(String) - Method in class net.sf.basedb.clients.web.taglib.Icon

setImage(String) - Method in class net.sf.basedb.clients.web.taglib.table.Button

setImage(String) - Method in class net.sf.basedb.clients.web.taglib.table.Label

setImage(String) - Method in class net.sf.basedb.clients.web.taglib.Zoom

setImage(String) - Method in class net.sf.basedb.core.data.PlateMappingData

setImage(String) - Method in class net.sf.basedb.core.PlateMapping

Set the name of a small image that is a graphical representation of the mapping.

setImageRemapDir(String) - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory

setImpersonated(boolean) - Method in class net.sf.basedb.core.data.SessionData

setInactive(boolean) - Method in class net.sf.basedb.core.data.KitData

setInactive(boolean) - Method in class net.sf.basedb.core.Kit

Set the inactive flag.

setInclude(int) - Method in class net.sf.basedb.core.data.ContextData

setInclude(int) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData

setInclude(String) - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory

setInclude(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory

setInclude(Collection<Include>) - Method in class net.sf.basedb.util.listable.TransformContext

setInclude(Set<Include>, String, Include) - Static method in class net.sf.basedb.clients.web.Base

Set include option if option parameter isn't null.

setIncludeDefault(boolean) - Method in class net.sf.basedb.core.FastAnnotationLoader

If the annotation type supports project-specific annotations this method can be used to control which values that are loaded.

setIncludeInherited(boolean) - Method in class net.sf.basedb.core.AnnotationRestriction.Options

setIncludePrimary(boolean) - Method in class net.sf.basedb.core.AnnotationRestriction.Options

setIncludes(Collection<Include>) - Method in class net.sf.basedb.core.AbstractEntityQuery

setIncludes(Collection<Include>) - Method in interface net.sf.basedb.core.query.EntityQuery

Clears the lists of includes and adds a new collection.

setIndex(float) - Method in class net.sf.basedb.util.extensions.ExtensionBean

setIndex(int) - Method in class net.sf.basedb.core.BioPlateEventParticipant

Set the index of the plate in this event.

setIndex(int) - Method in class net.sf.basedb.core.data.BioPlateEventParticipantData

setInheritedFrom(AnnotationData) - Method in class net.sf.basedb.core.data.AnnotationData

setInheritedFrom(AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

Set the primary annotation for an inherited annotation.

setInheritingAnnotations(Set<AnnotationData>) - Method in class net.sf.basedb.core.data.AnnotationData

setInitial(String) - Method in class net.sf.basedb.clients.web.taglib.HideableSection

setInputStream(InputStream) - Method in class net.sf.basedb.util.bfs.AnnotationParser

Set the input stream that should be parsed.

setInputStream(InputStream) - Method in class net.sf.basedb.util.bfs.DataParser

Set the input stream that should be parsed.

setInputStream(InputStream) - Method in class net.sf.basedb.util.bfs.MetadataParser

Set the input stream that should be parsed.

setInputStream(InputStream, String) - Method in class net.sf.basedb.util.parser.FlatFileParser

Set the input stream that will be parsed.

setInputStreamLocator(InputStreamLocator) - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter

Set the input stream locator that is responsible for opening files that are referenced from the metadata file.

setInstalled() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile

Mark the file as installed.

setInstalledFile(File) - Method in class net.sf.basedb.util.extensions.manager.Settings

Mark the given file as installed by the extension system.

setInstalledSchemaVersion(int) - Method in class net.sf.basedb.core.hibernate.SessionFactoryConfiguration

Deprecated.

Callback intended for BASE core to set the installed schema version.

setInteger(int, int) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setInteger(String, int) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setIntegerValues(List<Integer>) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink

setIntensities(FlatFileParser.Data, float[], int) - Method in class net.sf.basedb.util.importer.spotdata.GenericIntensityParser

setIntensities(FlatFileParser.Data, float[], int) - Method in class net.sf.basedb.util.importer.spotdata.MAParser

setIntensities(FlatFileParser.Data, float[], int) - Method in interface net.sf.basedb.util.importer.spotdata.SpotIntensityParser

Extract the intensity values from the current data line for a single bioassay.

setIntensityTransform(int) - Method in class net.sf.basedb.core.data.BioAssaySetData

setIntensityTransform(IntensityTransform) - Method in class net.sf.basedb.core.BioAssaySet

Sets the transform used on the spot intensities before they were stored in the database.

setIntensityTransform(IntensityTransform) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter

Set the intensity transform that have been applied to the spot data in the file.

setInteractive(boolean) - Method in class net.sf.basedb.core.data.PluginDefinitionData

setInteractive(boolean) - Method in class net.sf.basedb.core.PluginDefinition

setInterfaceName(String) - Method in class net.sf.basedb.core.data.PluginTypeData

setInterfaceName(String) - Method in class net.sf.basedb.core.PluginType

The class name cannot be changed.

setInternalId(int) - Method in class net.sf.basedb.util.extensions.xml.PluginInfo

setInternalName(String) - Method in class net.sf.basedb.core.data.FileData

setInternalName(String) - Method in class net.sf.basedb.core.File

Set the internal name of this file.

setInterruptHandler(InterruptHandler) - Static method in class net.sf.basedb.core.signal.ThreadSignalHandler

Register an interrupt handler with the current thread.

setInterval(String) - Method in class net.sf.basedb.clients.web.extensions.service.DummyService

Set the interval between writes to stdout.

setItem(int, Item) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

setItem(Object) - Method in class net.sf.basedb.clients.web.taglib.extensions.Render

setItem(Object) - Method in class net.sf.basedb.clients.web.taglib.PropertyValue

setItem(Object) - Method in class net.sf.basedb.clients.web.taglib.table.ExtensionCells

setItem(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

Set the item type to check the permission for.

setItem(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

Set the item type to check the permission for.

setItem(Annotatable) - Method in class net.sf.basedb.core.AnnotationSet

Set the item this annotation set belongs to.

setItem(FileStoreEnabled) - Method in class net.sf.basedb.core.FileSet

Set the item this file set belongs to.

setItem(Item) - Method in class net.sf.basedb.clients.web.taglib.table.Table

setItem(Subtypable) - Method in class net.sf.basedb.clients.web.taglib.SubtypeSelector

setItemId(int) - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData

setItemId(int) - Method in class net.sf.basedb.core.data.ContextData

setItemId(Integer) - Method in class net.sf.basedb.core.data.AnnotationSetData

setItemKey(ItemKeyData) - Method in interface net.sf.basedb.core.data.ShareableData

Set the ItemKeyData for the item.

setItemKey(ItemKeyData) - Method in class net.sf.basedb.core.data.SharedData

setItemKey(DbControl, ShareableData, ItemKey) - Static method in class net.sf.basedb.core.ShareableUtil

Set the item key of a ShareableData object.

setItemKey(ItemKey) - Method in interface net.sf.basedb.core.Shareable

Set the ItemKey for this item.

setItemKey(ItemKey) - Method in class net.sf.basedb.core.SharedItem

setItemKeys(Set<ItemKeyData>) - Method in class net.sf.basedb.core.data.GroupData

setItemKeys(Set<ItemKeyData>) - Method in class net.sf.basedb.core.data.UserData

setItemList(ItemListData) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData

setItemPermission(Permission) - Method in class net.sf.basedb.core.AbstractEntityQuery

setItemPermission(Permission) - Method in class net.sf.basedb.core.ItemContext

Specify the permission the logged in user must have for items returned by a query.

setItemPermission(Permission) - Method in interface net.sf.basedb.core.query.EntityQuery

Only return items which the logged in user has the specified permission for.

setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.AnnotationTypeCategoryData

setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.BioMaterialData

setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.BioPlateTypeData

setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.ContextData

setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.DerivedBioAssayData

setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.FileData

setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.HardwareData

setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.ItemListData

setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData

setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.ItemSubtypeFileTypeData

setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.JobData

setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.KitData

setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.PhysicalBioAssayData

setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.ProtocolData

setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.SoftwareData

setItemSubtype(ItemSubtypeData) - Method in interface net.sf.basedb.core.data.SubtypableData

Set the subtype of the item.

setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.TagData

setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.AnnotationTypeCategory

Set the item subtype that is linked to this category of annotations.

setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.BioMaterial

setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.BioPlateType

Set the subtype that biomaterial items should have when placed on a plate with the bioplate type.

setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.DerivedBioAssay

setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.File

setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.Hardware

setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.ItemContext

Set a subtype to relate to this context.

setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.ItemList

Set the subtype of items that can be members in this list.

setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.ItemSubtype

Do nothing.

setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.Job

setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.Kit

setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.PhysicalBioAssay

setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.Protocol

setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.Software

setItemSubtype(ItemSubtype) - Method in interface net.sf.basedb.core.Subtypable

Set the subtype on the item.

setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.Tag

setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.util.annotations.InheritSpecification

Set the subtype a parent item must have if annotations should be inherited from it.

setItemSubtypes(Set<ItemSubtypeFileTypeData>) - Method in class net.sf.basedb.core.data.DataFileTypeData

setItemtype(Item) - Method in class net.sf.basedb.clients.web.taglib.SubtypeSelector

setItemType(int) - Method in class net.sf.basedb.core.data.AnnotationSetData

setItemType(int) - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData

setItemType(int) - Method in class net.sf.basedb.core.data.ContextData

setItemType(int) - Method in class net.sf.basedb.core.data.ContextIndex

setItemType(int) - Method in class net.sf.basedb.core.data.DataFileTypeData

setItemType(int) - Method in class net.sf.basedb.core.data.DiskUsageData

setItemType(int) - Method in class net.sf.basedb.core.data.FileSetData

setItemType(int) - Method in class net.sf.basedb.core.data.GuiContextData

setItemType(int) - Method in class net.sf.basedb.core.data.ItemSubtypeData

setItemType(int) - Method in class net.sf.basedb.core.data.RoleKeyData

setItemType(Item) - Method in class net.sf.basedb.core.DataFileType

setItemType(Item) - Method in class net.sf.basedb.core.query.QueryParameter

Changes the type of the parameter.

setItemTypes(Collection<Item>) - Method in class net.sf.basedb.core.AnnotationType

Enable the annotation type for all of the specified item and disable it for all other.

setItemTypes(Set<Integer>) - Method in class net.sf.basedb.core.data.AnnotationTypeData

setJarFile(String) - Method in class net.sf.basedb.core.data.PluginDefinitionData

setJarFile(String) - Method in class net.sf.basedb.core.data.PluginTypeData

setJarFile(String) - Method in class net.sf.basedb.core.PluginDefinition

The jar path cannot be changed.

setJarFile(String) - Method in class net.sf.basedb.core.PluginType

The jar path cannot be changed.

setJdbcBatchSize(Integer) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

setJdbcBatchSize(Integer) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

setJep(String) - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField

Set the expression used to select data in the query.

setJob(JobData) - Method in class net.sf.basedb.core.data.ArrayDesignData

setJob(JobData) - Method in class net.sf.basedb.core.data.ChangeHistoryData

setJob(JobData) - Method in class net.sf.basedb.core.data.DerivedBioAssayData

setJob(JobData) - Method in class net.sf.basedb.core.data.ExtraValueData

setJob(JobData) - Method in class net.sf.basedb.core.data.MessageData

setJob(JobData) - Method in class net.sf.basedb.core.data.RawBioAssayData

setJob(JobData) - Method in class net.sf.basedb.core.data.TransformationData

setJob(JobData) - Method in class net.sf.basedb.core.Message

setJob(Job) - Method in class net.sf.basedb.core.DerivedBioAssay

Set the job on this derived bioassay that was used to create or import data for it.

setJob(Job) - Method in class net.sf.basedb.core.ExtraValue

Set the job that created the extra values.

setJob(Job) - Method in class net.sf.basedb.core.RawBioAssay

Set the job on this raw bioassay that was used to create or import data for it.

setJob(Job) - Method in class net.sf.basedb.core.Transformation

Set the job that executed this transformation.

setJobAgent(JobAgentData) - Method in class net.sf.basedb.core.data.JobAgentSettingsData

setJobAgent(JobAgent) - Method in class net.sf.basedb.core.Job

Set the job agent this job should run on.

setJobAgent(JobAgent) - Method in class net.sf.basedb.core.JobAgentSettings

setJobAgentId(Integer) - Method in class net.sf.basedb.core.data.JobData

setJobAgentSettings(Set<JobAgentSettingsData>) - Method in class net.sf.basedb.core.data.PluginDefinitionData

setJobId(Integer) - Method in class net.sf.basedb.core.data.ChangeHistoryData

setJobs(Set<JobData>) - Method in class net.sf.basedb.core.data.ExperimentData

setJspcontext(JspContext) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

setJspContext(JspContext) - Method in class net.sf.basedb.clients.web.extensions.edit.AbstractOnSaveAction

Get the JSP context of the current invokation.

setKeepSkippedLines(boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser

If the FlatFileParser.nextData() and FlatFileParser.hasMoreData() methods should keep information of lines that was skipped because they matched the ignore pattern or could be interpreted as data lines.

setKeyId(int) - Method in class net.sf.basedb.core.data.keyring.KeyPermission

Set the id of the key.

setKeyId(int) - Method in class net.sf.basedb.core.data.keyring.PluginKeys

Sets the id of the RoleKey

setKeys(Set<RoleKeyData>) - Method in class net.sf.basedb.core.data.RoleData

setKit(KitData) - Method in class net.sf.basedb.core.data.BioMaterialEventData

setKit(KitData) - Method in class net.sf.basedb.core.data.BioPlateEventData

setKit(KitData) - Method in class net.sf.basedb.core.data.DerivedBioAssayData

setKit(Kit) - Method in class net.sf.basedb.core.BioMaterialEvent

Set the Kit that was used in this event.

setKit(Kit) - Method in class net.sf.basedb.core.BioPlateEvent

Set the Kit that was used in this event.

setKit(Kit) - Method in class net.sf.basedb.core.DerivedBioAssay

Set the Kit that was used when creating this bioassay.

setLabel(String) - Method in class net.sf.basedb.core.data.ParameterValueData

setLastModified(Date) - Method in class net.sf.basedb.util.uri.UriMetadata

setLastProcessResults(ProcessResults) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager

Save the last process results so that they can be used later on.

setLastRemoteId(String) - Method in class net.sf.basedb.core.data.UserDeviceData

setLastSource(String) - Method in class net.sf.basedb.core.data.ReporterData

setLastSyncProperties(String) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData

setLastUpdate(Date) - Method in class net.sf.basedb.core.data.AnnotationData

setLastUpdate(Date) - Method in class net.sf.basedb.core.data.FileData

setLastUpdate(Date) - Method in class net.sf.basedb.core.data.ReporterData

setLastUpdated() - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlot

setLastUsed(Date) - Method in class net.sf.basedb.core.data.UserDeviceData

setLatitude(Float) - Method in class net.sf.basedb.util.GeoLocation

setLayerNo(short) - Method in class net.sf.basedb.core.data.DataCubeLayerData

setLayerNo(short) - Method in class net.sf.basedb.core.DataCubeLayer

setLayers(Set<DataCubeLayerData>) - Method in class net.sf.basedb.core.data.DataCubeData

setLength(int) - Method in class net.sf.basedb.core.data.ReporterClonePropertyData

setLength(Long) - Method in class net.sf.basedb.util.uri.UriMetadata

setLevel(String) - Method in class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory

Set the level of the error handler.

setLimit(int) - Method in class net.sf.basedb.core.signal.ProgressReporterSignalHandler

Set the percentage limit.

setLinkName(String) - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics

setList(Collection<?>) - Method in class net.sf.basedb.clients.web.taglib.table.CellValue

setLocale(int, Locale) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setLocale(String, Locale) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setLocation(int) - Method in class net.sf.basedb.core.data.DiskUsageData

setLocation(int) - Method in class net.sf.basedb.core.data.FileData

setLocation(int) - Method in class net.sf.basedb.core.data.QuotaIndex

setLocation(String) - Method in class net.sf.basedb.core.data.SessionData

setLocation(String) - Method in class net.sf.basedb.core.data.UserDeviceData

setLocation(Location) - Method in class net.sf.basedb.core.File

Set the location of this File item.

setLocationLatitude(Float) - Method in class net.sf.basedb.core.data.SessionData

setLocationLatitude(Float) - Method in class net.sf.basedb.core.data.UserDeviceData

setLocationLongitude(Float) - Method in class net.sf.basedb.core.data.SessionData

setLocationLongitude(Float) - Method in class net.sf.basedb.core.data.UserDeviceData

setLocked(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Navigator

setLocked(boolean) - Method in class net.sf.basedb.core.data.ReporterCloneTemplateData

setLockMode(int) - Method in class net.sf.basedb.core.data.BioPlateTypeData

setLockMode(String, LockMode) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setLockMode(String, LockMode) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setLockMode(LockModeType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setLockMode(LockModeType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setLockMode(BioWell.LockMode) - Method in class net.sf.basedb.core.BioPlateType

Set the lock mode for wells on plates of this plate type.

setLockOptions(LockOptions) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setLockOptions(LockOptions) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setLogarithmic(boolean) - Method in class net.sf.basedb.core.Coloring

Specify if we should take the logarithm of values before the color is generated or not.

setLogarithmic(boolean) - Method in class net.sf.basedb.core.data.ColoringData

setLogin(String) - Method in class net.sf.basedb.core.authentication.LoginRequest

Set the login name to use.

setLogin(String) - Method in class net.sf.basedb.core.data.UserData

setLogin(String) - Method in class net.sf.basedb.core.User

Set the login for the user account.

setLoginComment(String) - Method in class net.sf.basedb.core.data.SessionData

setLoginField(FieldInfo) - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean

setLoginTime(Date) - Method in class net.sf.basedb.core.data.SessionData

setLogoutTime(Date) - Method in class net.sf.basedb.core.data.SessionData

setLong(int, long) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setLong(String, long) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setLongitude(Float) - Method in class net.sf.basedb.util.GeoLocation

setLongValues(List<Long>) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink

setMainItemType(Item) - Method in class net.sf.basedb.core.ItemSubtype

setMainType(int) - Method in class net.sf.basedb.core.data.PluginDefinitionData

setMainType(Plugin.MainType) - Method in class net.sf.basedb.core.PluginDefinition

The type cannot be changed.

setMandatory(boolean) - Method in class net.sf.basedb.core.data.ReporterClonePropertyData

setMappings(short) - Method in class net.sf.basedb.core.data.VirtualDbData

setMasked(boolean) - Method in class net.sf.basedb.core.data.ParameterValueData

setMasterParser(AnnotationParser) - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser

Sets the master parser.

setMatchingSource(int) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData

setMatchingTransformed(int) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData

setMaxAge(int) - Method in class net.sf.basedb.core.DiskUsageStatistics

Set the max age in seconds for a disk usage summary object before it is reloaded from the database again.

setMaxBaseVersion(String) - Method in class net.sf.basedb.util.extensions.AboutBean

setMaxBytes(long) - Method in class net.sf.basedb.core.data.QuotaIndex

setMaxcharacters(int) - Method in class net.sf.basedb.clients.web.taglib.table.Cell

setMaxDataColumns(int) - Method in class net.sf.basedb.util.parser.FlatFileParser

Set the maximum number of columns a data line can contain in order for it to be counted as a data line.

setMaxheight(String) - Method in class net.sf.basedb.clients.web.taglib.table.Cell

setMaxLength(Integer) - Method in class net.sf.basedb.core.AnnotationType

Set the maximum allowed string length for a Type.STRING annotation.

setMaxMemory(Long) - Method in class net.sf.basedb.core.data.JobAgentSettingsData

setMaxMemory(Long) - Method in class net.sf.basedb.core.data.PluginDefinitionData

setMaxMemory(Long) - Method in class net.sf.basedb.core.JobAgentSettings

Set maximim amount of memory the plugin is allowed to use.

setMaxMemory(Long) - Method in class net.sf.basedb.core.PluginDefinition

Set the maximum amount of memory the plugin is allowed to use.

setMaxRandomSamples(int) - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics.Options

Set the maximum number of items to use for gathering the statistics.

setMaxRawMappingsForSpot(int) - Method in class net.sf.basedb.core.data.DataCubeData

setMaxResults(int) - Method in class net.sf.basedb.core.AbstractQuery

setMaxResults(int) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setMaxResults(int) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setMaxResults(int) - Method in interface net.sf.basedb.core.query.Query

Specify that the query should at most return the specified number of rows.

setMaxUnknownLines(int) - Method in class net.sf.basedb.util.parser.FlatFileParser

The number of unknown lines in a row that can be parsed by the parseHeaders method before it gives up.

setMaxValue(Float) - Method in class net.sf.basedb.core.Coloring

Set the value that represents the maximum value.

setMaxValue(Float) - Method in class net.sf.basedb.core.data.ColoringData

setMaxValueDouble(Double) - Method in class net.sf.basedb.core.AnnotationType

Set the maximum allowed value for a Type.FLOAT or Type.DOUBLE annotation.

setMaxValueLong(Long) - Method in class net.sf.basedb.core.AnnotationType

Set the maximum allowed value for an Type.INT or Type.LONG annotation.

setMaxwidth(String) - Method in class net.sf.basedb.clients.web.taglib.table.Cell

setMd5(String) - Method in class net.sf.basedb.core.data.FileData

setMd5(String) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData

setMd5(String) - Method in class net.sf.basedb.util.uri.UriMetadata

setMd5AtLastSync(String) - Method in class net.sf.basedb.core.data.ItemListData

setMember(File, DataFileType) - Method in class net.sf.basedb.core.FileSet

Set a file of a given type as a member of this file set.

setMembers(Set<Integer>) - Method in class net.sf.basedb.core.data.ItemListData

setMembers(Set<FileSetMemberData>) - Method in class net.sf.basedb.core.data.FileSetData

setMemberType(int) - Method in class net.sf.basedb.core.data.ItemListData

setMemberType(Item) - Method in class net.sf.basedb.core.ItemList

setMenu(String) - Method in class net.sf.basedb.clients.web.taglib.Page

setMenuId(String) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

setMenuId(String) - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean

setMenuId(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

setMessage(String) - Method in class net.sf.basedb.core.ItemContext

Set a message to be displayed by a client application as soon as it is appropriate to do so.

setMessagePrefix(String) - Method in class net.sf.basedb.util.ChainedProgressReporter

Set a message prefix that is pre-pended to message before it is sent to the master progress reporter.

setMessages(Set<MessageData>) - Method in class net.sf.basedb.core.data.JobData

setMessages(Set<MessageData>) - Method in class net.sf.basedb.core.data.UserData

setMetadataFromURI(UriMetadata) - Method in class net.sf.basedb.core.File

setMetadataParser(MetadataParser) - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter

Set the metadata file parser.

setMetadataPrefix(String) - Method in class net.sf.basedb.util.basefile.BaseFileWriter

Change the metadata prefix string.

setMetadataWriter(MetadataWriter) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter

Set the stream were the metadata should be written.

setMetaGrid(int, int) - Method in class net.sf.basedb.core.ArrayDesignBlock

Set the metagrid coordinates.

setMetaGridX(int) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData

setMetaGridX(Integer) - Method in class net.sf.basedb.core.data.RawData

setMetaGridX(Integer) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock

setMetaGridY(int) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData

setMetaGridY(Integer) - Method in class net.sf.basedb.core.data.RawData

setMetaGridY(Integer) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock

setMidValue(Float) - Method in class net.sf.basedb.core.Coloring

Set the value that represents the midpoint value.

setMidValue(Float) - Method in class net.sf.basedb.core.data.ColoringData

setMimeType(String) - Method in class net.sf.basedb.clients.web.util.ServletExportOutputStream

Calls ServletResponse.setContentType(String)

setMimeType(String) - Method in class net.sf.basedb.core.data.FileData

setMimeType(String) - Method in class net.sf.basedb.core.File

Set the mime type for this File item.

setMimeType(String) - Method in class net.sf.basedb.core.plugin.ExportOutputStream

Do nothing.

setMimeType(String) - Method in class net.sf.basedb.util.FileExportOutputStream

Calls File.setMimeType(String)

setMimeType(String) - Method in class net.sf.basedb.util.uri.UriMetadata

setMimeTypeAuto(String, ItemSubtype) - Method in class net.sf.basedb.core.File

Set the mime type automatically by checking the extension of the name.

setMinBaseVersion(String) - Method in class net.sf.basedb.util.extensions.AboutBean

setMinCount(int) - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics.Options

Do not return information about links with a count that is less than this value.

setMinDataColumns(int) - Method in class net.sf.basedb.util.parser.FlatFileParser

Set the minimum number of columns a data line must contain in order for it to be counted as a data line.

setMinFraction(int) - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics.Options

Do not return information about links if they are found on less than the specified fraction of samples.

setMinValue(Float) - Method in class net.sf.basedb.core.Coloring

Set the value that represents the minimum value.

setMinValue(Float) - Method in class net.sf.basedb.core.data.ColoringData

setMinValueDouble(Double) - Method in class net.sf.basedb.core.AnnotationType

Set the minimum allowed value for a Type.FLOAT or Type.DOUBLE annotation.

setMinValueLong(Long) - Method in class net.sf.basedb.core.AnnotationType

Set the minimum allowed value for an Type.INT or Type.LONG annotation.

setMode(boolean, boolean) - Method in class net.sf.basedb.util.basefile.BaseFileWriter

setMore(JSONObject, T) - Method in class net.sf.basedb.util.json.EnumConverter

Can be used by subclasses to set more properties on the JSON object.

setMore(JSONObject, T) - Method in class net.sf.basedb.util.json.NameableConverter

Can be used by subclasses to set more properties on the JSON object.

setMoreDynamicAttributes(Iterator<DynamicActionAttribute>) - Method in class net.sf.basedb.clients.web.taglib.StylableTag

setMultiple(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

setMultiple(boolean) - Method in class net.sf.basedb.plugins.executor.ParameterDefinition

Set if this parameter can have multiple values or only one.

setMultiplicity(int) - Method in class net.sf.basedb.core.AnnotationType

Set the multiplicity.

setMultiplicity(int) - Method in class net.sf.basedb.core.data.AnnotationTypeData

setMultiuserAccount(boolean) - Method in class net.sf.basedb.core.data.UserData

setMultiuserAccount(boolean) - Method in class net.sf.basedb.core.User

Sets if the user account is multiuser account.

setName(int) - Method in class net.sf.basedb.clients.web.taglib.Input

setName(String) - Method in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory

setName(String) - Method in class net.sf.basedb.clients.web.extensions.startpage.StartPageBean

setName(String) - Method in class net.sf.basedb.clients.web.taglib.Input

setName(String) - Method in class net.sf.basedb.clients.web.taglib.table.Hidden

setName(String) - Method in class net.sf.basedb.core.AnyToAny

setName(String) - Method in class net.sf.basedb.core.authentication.ExtraUserInformation

setName(String) - Method in class net.sf.basedb.core.BioAssay

setName(String) - Method in class net.sf.basedb.core.BioAssaySet

setName(String) - Method in class net.sf.basedb.core.BioPlateEventType

setName(String) - Method in class net.sf.basedb.core.BioPlateType

setName(String) - Method in class net.sf.basedb.core.CommonItem

setName(String) - Method in class net.sf.basedb.core.data.AnyToAnyData

setName(String) - Method in class net.sf.basedb.core.data.BioAssayData

setName(String) - Method in class net.sf.basedb.core.data.BioAssaySetData

setName(String) - Method in class net.sf.basedb.core.data.BioPlateEventTypeData

setName(String) - Method in class net.sf.basedb.core.data.BioPlateTypeData

setName(String) - Method in class net.sf.basedb.core.data.ChangeHistoryData

setName(String) - Method in class net.sf.basedb.core.data.CommonData

setName(String) - Method in class net.sf.basedb.core.data.ContextData

setName(String) - Method in class net.sf.basedb.core.data.ContextIndex

setName(String) - Method in class net.sf.basedb.core.data.DataFileTypeData

setName(String) - Method in class net.sf.basedb.core.data.ExtraValueTypeData

setName(String) - Method in class net.sf.basedb.core.data.GroupData

setName(String) - Method in class net.sf.basedb.core.data.HelpData

setName(String) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData

setName(String) - Method in class net.sf.basedb.core.data.ItemSubtypeData

setName(String) - Method in class net.sf.basedb.core.data.MessageData

setName(String) - Method in class net.sf.basedb.core.data.MimeTypeData

setName(String) - Method in interface net.sf.basedb.core.data.NameableData

Set the name of the item.

setName(String) - Method in class net.sf.basedb.core.data.NewsData

setName(String) - Method in class net.sf.basedb.core.data.PlateEventTypeData

setName(String) - Method in class net.sf.basedb.core.data.PlateGeometryData

setName(String) - Method in class net.sf.basedb.core.data.PlatformData

setName(String) - Method in class net.sf.basedb.core.data.PlatformVariantData

setName(String) - Method in class net.sf.basedb.core.data.PluginDefinitionData

setName(String) - Method in class net.sf.basedb.core.data.PluginTypeData

setName(String) - Method in class net.sf.basedb.core.data.ProjectData

setName(String) - Method in class net.sf.basedb.core.data.QuantityData

setName(String) - Method in class net.sf.basedb.core.data.QuotaData

setName(String) - Method in class net.sf.basedb.core.data.QuotaTypeData

setName(String) - Method in class net.sf.basedb.core.data.ReporterData

setName(String) - Method in class net.sf.basedb.core.data.ReporterTypeData

setName(String) - Method in class net.sf.basedb.core.data.RoleData

setName(String) - Method in class net.sf.basedb.core.data.RoleKeyData

setName(String) - Method in class net.sf.basedb.core.data.RootRawBioAssayData

setName(String) - Method in class net.sf.basedb.core.data.SettingData

setName(String) - Method in class net.sf.basedb.core.data.TransformationData

setName(String) - Method in class net.sf.basedb.core.data.UnitData

setName(String) - Method in class net.sf.basedb.core.data.UserData

setName(String) - Method in class net.sf.basedb.core.data.UserDeviceData

setName(String) - Method in class net.sf.basedb.core.data.VersionedParameter

setName(String) - Method in class net.sf.basedb.core.DataFileType

setName(String) - Method in class net.sf.basedb.core.Directory

setName(String) - Method in class net.sf.basedb.core.ExtraValueType

setName(String) - Method in class net.sf.basedb.core.File

setName(String) - Method in class net.sf.basedb.core.Group

setName(String) - Method in class net.sf.basedb.core.Help

setName(String) - Method in class net.sf.basedb.core.ItemSubtype

setName(String) - Method in class net.sf.basedb.core.Message

setName(String) - Method in class net.sf.basedb.core.MimeType

setName(String) - Method in interface net.sf.basedb.core.Nameable

Set the name of the item.

setName(String) - Method in class net.sf.basedb.core.News

setName(String) - Method in class net.sf.basedb.core.PlateEventType

setName(String) - Method in class net.sf.basedb.core.PlateGeometry

setName(String) - Method in class net.sf.basedb.core.Platform

setName(String) - Method in class net.sf.basedb.core.PlatformVariant

setName(String) - Method in class net.sf.basedb.core.PluginType

setName(String) - Method in class net.sf.basedb.core.Project

setName(String) - Method in class net.sf.basedb.core.Quantity

setName(String) - Method in class net.sf.basedb.core.Quota

setName(String) - Method in class net.sf.basedb.core.QuotaType

setName(String) - Method in class net.sf.basedb.core.RawDataType

Update the name.

setName(String) - Method in class net.sf.basedb.core.ReporterType

setName(String) - Method in class net.sf.basedb.core.Role

setName(String) - Method in class net.sf.basedb.core.RoleKey

setName(String) - Method in class net.sf.basedb.core.RootRawBioAssay

setName(String) - Method in class net.sf.basedb.core.Setting

Set the name for this setting.

setName(String) - Method in class net.sf.basedb.core.SyncFilter

setName(String) - Method in class net.sf.basedb.core.Transformation

setName(String) - Method in class net.sf.basedb.core.Unit

setName(String) - Method in class net.sf.basedb.core.User

setName(String) - Method in class net.sf.basedb.core.UserDevice

setName(String) - Method in class net.sf.basedb.plugins.executor.ParameterDefinition

Set the name of the parameter.

setName(String) - Method in class net.sf.basedb.util.extensions.AboutBean

setName(String) - Method in class net.sf.basedb.util.extensions.ExtensionPointBean

setName(String) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay

Set the name of the child bioassay.

setName(NameableData, String) - Static method in class net.sf.basedb.core.NameableUtil

Set the name of a NameableData object.

setNeedResourcesPerExtension(boolean) - Method in class net.sf.basedb.clients.web.extensions.JspContext

Set a flag indicating that resources (eg. scripts and stylesheets) should be tracked per extension.

setNewAnnotations(AnnotationFlatFileImporter, AnnotationBatcher, boolean, boolean, boolean, boolean) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations

Annotate the item with the annotation values from the file.

setNewitem(boolean) - Method in class net.sf.basedb.clients.web.taglib.Select

setNewsDate(Date) - Method in class net.sf.basedb.core.data.NewsData

setNewsDate(Date) - Method in class net.sf.basedb.core.News

Set the date that is shown in listings.

setNewValue(String) - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData

setNextCommand(String) - Method in class net.sf.basedb.core.PluginRequest

Sets the next command in a configuration sequence.

setNode(String) - Method in class net.sf.basedb.core.data.JobData

setNoDuplicates(boolean) - Method in class net.sf.basedb.util.annotations.InheritSpecification

If this flag is set (default=true), only one annotation of the specified annotation type can be inherited.

setNoProject() - Method in class net.sf.basedb.core.snapshot.SnapshotManager

Revert to the default bahavior for loading project-specific annotations.

setNoskin(boolean) - Method in class net.sf.basedb.clients.web.taglib.Page

Set to TRUE to disable skins.

setNotabs(boolean) - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl

setNotFound(boolean) - Method in class net.sf.basedb.util.extensions.xml.PluginInfo

setNotNullDate(Date, String) - Static method in class net.sf.basedb.core.DateUtil

Make a copy of a Date object.

setNotNullString(String, String, int) - Static method in class net.sf.basedb.core.StringUtil

Trim and check the length of a string.

setNullable(boolean) - Method in class net.sf.basedb.core.data.ReporterClonePropertyData

setNullableDate(Date, String) - Static method in class net.sf.basedb.core.DateUtil

Make a copy of a Date object.

setNullableString(String, String, int) - Static method in class net.sf.basedb.core.StringUtil

Trim and check the length of a string.

setNulltext(String) - Method in class net.sf.basedb.clients.web.taglib.PropertyValue

setNullValue(String) - Method in class net.sf.basedb.util.export.TableWriter

Change the null value string.

setNumArrays(int) - Method in class net.sf.basedb.core.ArrayDesign

Set the number of arrays on a single slide.

setNumArrays(int) - Method in class net.sf.basedb.core.data.ArrayDesignData

setNumberFormat(Formatter<Number>) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil

Set a formatter that is used for formatting cells with numeric values.

setNumColumns(int) - Method in class net.sf.basedb.clients.web.taglib.table.Table

setNumColumns(int) - Method in class net.sf.basedb.util.bfs.DataParser

Set the number of data columns that are expected to be found in this file.

setNumColumns(short) - Method in class net.sf.basedb.core.data.DataCubeData

setNumDbFeatures(int) - Method in class net.sf.basedb.core.data.ArrayDesignData

setNumDecimals(SessionControl, int) - Static method in class net.sf.basedb.clients.web.formatter.FormatterSettings

Set the number of decimals a number formatter should display.

setNumExtraValues(short) - Method in class net.sf.basedb.core.data.DataCubeData

setNumFileFeatures(int) - Method in class net.sf.basedb.core.ArrayDesign

Set the number of features that are stored in files.

setNumFileFeatures(int) - Method in class net.sf.basedb.core.data.ArrayDesignData

setNumFileReporters(int) - Method in class net.sf.basedb.core.BioAssaySet

Set the number of unique reporters for data that is stored in files.

setNumFileReporters(int) - Method in class net.sf.basedb.core.data.BioAssaySetData

setNumFileSpots(int) - Method in class net.sf.basedb.core.BioAssay

Set the number of spots that are stored in files.

setNumFileSpots(int) - Method in class net.sf.basedb.core.BioAssaySet

Set the number of spots that are stored in files.

setNumFileSpots(int) - Method in class net.sf.basedb.core.data.BioAssayData

setNumFileSpots(int) - Method in class net.sf.basedb.core.data.BioAssaySetData

setNumFileSpots(int) - Method in class net.sf.basedb.core.data.RawBioAssayData

setNumFileSpots(int) - Method in class net.sf.basedb.core.RawBioAssay

Set the number of spots that are stored in files.

setNumFileValues(int) - Method in class net.sf.basedb.core.data.ExtraValueData

setNumFileValues(int) - Method in class net.sf.basedb.core.ExtraValue

Set the number of extra values that are stored in files.

setNumFilters(short) - Method in class net.sf.basedb.core.data.DataCubeData

setNumLayers(short) - Method in class net.sf.basedb.core.data.DataCubeData

setNumPositions(int) - Method in class net.sf.basedb.core.data.DataCubeData

setNumPositions(int) - Method in class net.sf.basedb.core.DataCube

Set by the AbstractBatcher.close() method.

setNumReporters(int) - Method in class net.sf.basedb.core.data.BioAssaySetData

setNumSpots(int) - Method in class net.sf.basedb.core.data.BioAssayData

setNumSpots(int) - Method in class net.sf.basedb.core.data.BioAssaySetData

setNumValues(int) - Method in class net.sf.basedb.core.data.ExtraValueData

setNumValues(int) - Method in class net.sf.basedb.core.ExtraValue

Called from batcher when it is closed.

setObject(String, Object) - Method in class net.sf.basedb.core.ItemContext

Set a value.

setOldValue(String) - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData

setOnClick(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

setOnItem(Subtypable) - Method in class net.sf.basedb.core.ItemSubtype

Helper method for implementing the Subtypable.setItemSubtype(ItemSubtype) method.

setOpen(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Menu

setOperator(int) - Method in class net.sf.basedb.core.data.PropertyFilterData

setOperator(Operator) - Method in class net.sf.basedb.core.PropertyFilter

Set the operator to use in the filter.

setOption(String, String) - Method in class net.sf.basedb.core.AnnotationType

Set an option.

setOption(String, String) - Method in class net.sf.basedb.plugins.executor.ParameterDefinition

Set the value for an option.

setOption(ValidationRuleAction, String, String) - Method in class net.sf.basedb.util.overview.ValidationOptions

Set an option for a validator rule.

setOptions(Map<String, String>) - Method in class net.sf.basedb.core.data.AnnotationTypeData

setOrAddFile(FileStoreEnabled, DataFileType, File) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Set or add a file to a file set.

setOrdinal(int) - Method in class net.sf.basedb.core.data.PlateEventTypeData

setOrdinal(int) - Method in class net.sf.basedb.core.PlateEventType

Set the order of this event in relation to the list of all events.

setOrganisation(String) - Method in class net.sf.basedb.core.authentication.ExtraUserInformation

setOrganisation(String) - Method in class net.sf.basedb.core.data.UserData

setOrganisation(String) - Method in class net.sf.basedb.core.User

Set the organisation this user works for, or null if unknown.

setOriginalBioMaterial(MeasuredBioMaterialData) - Method in class net.sf.basedb.core.data.BioWellData

setOriginalQuantity(Float) - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData

setOriginalQuantity(Float) - Method in class net.sf.basedb.core.MeasuredBioMaterial

Set the original quantity of the biomaterial.

setOriginX(int) - Method in class net.sf.basedb.core.ArrayDesignBlock

Set the distance from the left edge of the slide to the top left spot in this block.

setOriginX(int) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData

setOriginX(Integer) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock

setOriginY(int) - Method in class net.sf.basedb.core.ArrayDesignBlock

Set the distance from the top edge of the slide to the top left spot in this block.

setOriginY(int) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData

setOriginY(Integer) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock

setOutputStream(OutputStream) - Method in class net.sf.basedb.util.zip.Bzip2FilePacker

Wrap the output stream in a GZIPOutputStream.

setOutputStream(OutputStream) - Method in interface net.sf.basedb.util.zip.FilePacker

The output stream that the compressed files should be written to.

setOutputStream(OutputStream) - Method in class net.sf.basedb.util.zip.GzipFilePacker

Wrap the output stream in a GZIPOutputStream.

setOutputStream(OutputStream) - Method in class net.sf.basedb.util.zip.TarFilePacker

Wrap the output stream in a TarOutputStream.

setOutputStream(OutputStream) - Method in class net.sf.basedb.util.zip.ZipFilePacker

Wrap the output stream in a ZipOutputStream.

setOverrideId(int) - Method in class net.sf.basedb.core.data.AnnotationData

setOverrideId(int) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink

setOwner(OwnableData, User) - Static method in class net.sf.basedb.core.OwnableUtil

Set the owner of a OwnableData object.

setOwner(UserData) - Method in interface net.sf.basedb.core.data.OwnableData

Change the owner of the item.

setOwner(UserData) - Method in class net.sf.basedb.core.data.OwnedData

setOwner(DbControl, Set<OwnedItem>, User) - Static method in class net.sf.basedb.util.OwnableUtil

Change the owner of all specified items.

setOwner(DbControl, Item, Set<Integer>, User) - Static method in class net.sf.basedb.util.OwnableUtil

Change the owner of all specified items.

setOwner(User) - Method in interface net.sf.basedb.core.Ownable

Change the owner of the item.

setOwner(User) - Method in class net.sf.basedb.core.OwnedItem

setPage(int) - Method in class net.sf.basedb.clients.web.taglib.table.Navigator

setPage(int) - Method in class net.sf.basedb.core.data.ContextData

setPage(int) - Method in class net.sf.basedb.core.ItemContext

Set the current table page.

setPage(String) - Method in class net.sf.basedb.clients.web.taglib.table.Navigator

setPageContext(PageContext) - Method in class net.sf.basedb.clients.web.taglib.Head

setPageContext(PageContext) - Method in class net.sf.basedb.clients.web.taglib.Page

setPageContext(PageContext) - Method in class net.sf.basedb.clients.web.taglib.StylableTag

Reset the dynamic attributes to make sure old ones are not included in case the tag object is reused.

setPageContext(PageContext) - Method in class net.sf.basedb.clients.web.taglib.tab.Tab

Reset the dynamic attributes to make sure old ones are not included in case the tag object is reused.

setParameter(int, Object) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper

setParameter(int, Object) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setParameter(int, Object) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setParameter(int, Object, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setParameter(int, Object, Type) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper

setParameter(int, Object, Type) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setParameter(int, Object, Type) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setParameter(int, Instant, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setParameter(int, Instant, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setParameter(int, LocalDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setParameter(int, LocalDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setParameter(int, OffsetDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setParameter(int, OffsetDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setParameter(int, ZonedDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setParameter(int, ZonedDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setParameter(int, Calendar, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setParameter(int, Calendar, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setParameter(int, Date, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setParameter(int, Date, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setParameter(int, P, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setParameter(String, boolean, Object, Type) - Method in class net.sf.basedb.core.AbstractQuery

setParameter(String, Object) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper

setParameter(String, Object) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setParameter(String, Object) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setParameter(String, Object) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper

setParameter(String, Object, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setParameter(String, Object, Type) - Method in class net.sf.basedb.core.AbstractQuery

setParameter(String, Object, Type) - Method in interface net.sf.basedb.core.query.Query

Set the value of a query parameter.

setParameter(String, Object, Type) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper

setParameter(String, Object, Type) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setParameter(String, Object, Type) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setParameter(String, String) - Method in class net.sf.basedb.clients.web.extensions.AbstractJspFactory

Generic parameter setter metod.

setParameter(String, String) - Method in class net.sf.basedb.clients.web.extensions.ServletWrapper

Set the value of a servlet parameter.

setParameter(String, String) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter

Add a parameter that is exported in the 'settings' section, which is the first section in the BASEfile.

setParameter(String, String) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory

Set generic parameters.

setParameter(String, String) - Method in class net.sf.basedb.util.extensions.debug.ProxyActionFactory

Set generic parameters.

setParameter(String, String...) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter

Add a parameter that is exported in the [parameters] section.

setParameter(String, Instant, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setParameter(String, Instant, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setParameter(String, LocalDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setParameter(String, LocalDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setParameter(String, OffsetDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setParameter(String, OffsetDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setParameter(String, ZonedDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setParameter(String, ZonedDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setParameter(String, Calendar, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setParameter(String, Calendar, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setParameter(String, Date, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setParameter(String, Date, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setParameter(String, P, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setParameter(Parameter<Instant>, Instant, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setParameter(Parameter<Instant>, Instant, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setParameter(Parameter<LocalDateTime>, LocalDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setParameter(Parameter<LocalDateTime>, LocalDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setParameter(Parameter<OffsetDateTime>, OffsetDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setParameter(Parameter<OffsetDateTime>, OffsetDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setParameter(Parameter<ZonedDateTime>, ZonedDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setParameter(Parameter<ZonedDateTime>, ZonedDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setParameter(Parameter<Calendar>, Calendar, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setParameter(Parameter<Calendar>, Calendar, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setParameter(Parameter<Date>, Date, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setParameter(Parameter<Date>, Date, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setParameter(Parameter<P>, P) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setParameter(Parameter<T>, T) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper

setParameter(Parameter<T>, T) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setParameter(QueryParameter<P>, P) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setParameter(QueryParameter<P>, P, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setParameter(QueryParameter<P>, P, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setParameter(QueryParameter<P>, P, Type) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper

setParameter(QueryParameter<P>, P, Type) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setParameter(QueryParameter<P>, P, Type) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setParameter(QueryParameter<T>, T) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper

setParameter(QueryParameter<T>, T) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setParameterDefinition(ParameterDefinition) - Method in class net.sf.basedb.plugins.executor.ProgramParameter

setParameterList(int, Object[]) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setParameterList(int, Object[], Type) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setParameterList(int, Collection) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setParameterList(int, Collection, Type) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setParameterList(String, Object[]) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper

setParameterList(String, Object[]) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setParameterList(String, Object[]) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setParameterList(String, Object[], Type) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper

setParameterList(String, Object[], Type) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setParameterList(String, Object[], Type) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setParameterList(String, Collection) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper

setParameterList(String, Collection) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setParameterList(String, Collection) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setParameterList(String, Collection, Type) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper

setParameterList(String, Collection, Type) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setParameterList(String, Collection, Type) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setParameterList(QueryParameter<P>, Collection<P>) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper

setParameterList(QueryParameter<P>, Collection<P>) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setParameterList(QueryParameter<P>, Collection<P>) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setParameters(Object[], Type[]) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setParameters(PreparedStatement) - Method in class net.sf.basedb.core.AbstractSqlQuery.CountWork

setParameters(PreparedStatement) - Method in class net.sf.basedb.core.hibernate.ExecuteUpdateWork

This method should be overridden by subclasses that needs to set parameters on the statement that is going to be executed.

setParameters(PreparedStatement) - Method in class net.sf.basedb.core.hibernate.ResultSetWork

This method should be overridden by subclasses that needs to set parameters on the statement that is going to be executed.

setParameters(PreparedStatement, List<String>, int) - Method in class net.sf.basedb.core.AbstractSqlQuery

Set parameter values on a prepared statement.

setParameters(Map<String, ParameterValueData<?>>) - Method in class net.sf.basedb.core.data.JobData

setParameters(Set<AnnotationTypeData>) - Method in class net.sf.basedb.core.data.ProtocolData

setParameters(Query<?>, Map<String, QueryParameter>) - Method in class net.sf.basedb.core.AbstractHqlQuery

Set parameter values on a query.

setParameterValue(String, Object) - Method in class net.sf.basedb.core.PluginRequest

Set the value of a request parameter to a single value.

setParameterValue(String, String, String, ParameterType<?>, Object) - Method in class net.sf.basedb.core.Job

Set the value of a configuration parameter.

setParameterValue(String, ParameterType<?>, Object) - Method in class net.sf.basedb.core.Job

Set the value of a configuration parameter.

setParameterValue(PreparedStatement, int, Object, Type) - Method in class net.sf.basedb.core.AbstractSqlQuery

Set a parameter value on a prepared statement.

setParameterValues(String, String, String, ParameterType<?>, List<?>) - Method in class net.sf.basedb.core.Job

Set the value of a configuration parameter.

setParameterValues(String, String, String, ParameterType<?>, List<?>) - Method in class net.sf.basedb.core.PluginConfiguration

Set a configuration parameter.

setParameterValues(String, List<?>) - Method in class net.sf.basedb.core.PluginRequest

Set the value of a request parameter to a list of values.

setParameterValues(String, ParameterType<?>, List<?>) - Method in class net.sf.basedb.core.Job

Set the value of a configuration parameter.

setParameterValues(String, ParameterType<?>, List<?>) - Method in class net.sf.basedb.core.PluginConfiguration

Set a configuration parameter.

setParameterValues2(List<Element>) - Method in class net.sf.basedb.core.PluginConfiguration

Sets parameters for a PluginConfiguration from the elements in a xml configurations file.

setParameterValuesInternal(String, String, String, ParameterType<?>, List<?>, boolean) - Method in class net.sf.basedb.core.Job

Set the values of a configuration parameter.

setParameterValuesInternal(String, String, String, ParameterType<?>, List<?>, boolean) - Method in class net.sf.basedb.core.PluginConfiguration

Set the values of a configuration parameter.

setParameterVersion(int) - Method in class net.sf.basedb.core.data.JobData

setParameterVersion(int) - Method in class net.sf.basedb.core.data.PluginConfigurationData

setParent(BioMaterialData) - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData

setParent(DirectoryData) - Method in class net.sf.basedb.core.data.DirectoryData

setParent(WellData) - Method in class net.sf.basedb.core.data.WellData

setParent(Directory) - Method in class net.sf.basedb.core.Directory

Set the parent directory of this directory.

setParent(Well) - Method in class net.sf.basedb.core.Well

Set the parent well.

setParent(Renderer<? super A>) - Method in class net.sf.basedb.clients.web.extensions.renderer.PrefixSuffixRenderer

setParent(Renderer<? super A>) - Method in interface net.sf.basedb.util.extensions.WrappingRenderer

Set a parent renderer.

setParentBioAssay(DerivedBioAssayData) - Method in class net.sf.basedb.core.data.RawBioAssayData

setParentBioAssay(DerivedBioAssay) - Method in class net.sf.basedb.core.RawBioAssay

Set the DerivedBioAssay this raw bioassay is created from.

setParentExtract(ExtractData) - Method in class net.sf.basedb.core.data.RawBioAssayData

setParentExtract(Extract) - Method in class net.sf.basedb.core.RawBioAssay

Set the Extract this raw bioassay is created from.

setParentFilter(Filter<? super AnnotationSnapshot>) - Method in class net.sf.basedb.core.snapshot.DisabledInheritanceFilter

Set a parent filter that must also be passed in order for the this filter to pass an annotation.

setParentHasNullReporter(boolean) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo

Set a flag indicating that at least one position in the parent bioassay set has a null reporter.

setParentHasZeroReporter(boolean) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo

Set a flag indicating that at least one position in the parent bioassay set has a reporter with ID=0.

setParentId(int) - Method in class net.sf.basedb.core.data.keyring.GroupGroups

Set the id of the parent group.

setParents(Map<PlateData, Integer>) - Method in class net.sf.basedb.core.data.PlateData

setParents(Set<Integer>) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay

Set the parents for this child.

setParents(Set<BioAssayData>) - Method in class net.sf.basedb.core.data.BioAssayData

setParents(Set<DerivedBioAssayData>) - Method in class net.sf.basedb.core.data.DerivedBioAssayData

setParents(Set<GroupData>) - Method in class net.sf.basedb.core.data.GroupData

setParents(Set<ItemSubtypeData>) - Method in class net.sf.basedb.core.data.ItemSubtypeData

setParentSet(Set<PlateData>) - Method in class net.sf.basedb.core.data.PlateData

setParentType(Integer) - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData

setParseAllExcelSheets(boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser

If this flag is set and the source file is an Excel file, then all sheets will be parsed unless a named sheet specified.

setParser(int) - Method in class net.sf.basedb.core.data.FormulaData

setParser(Formula.Parser) - Method in class net.sf.basedb.core.Formula

Set the parser used to convert the formula to an expression or restriction.

setParticipants(Set<BioPlateEventParticipantData>) - Method in class net.sf.basedb.core.data.BioPlateEventData

setPassword(String) - Method in class net.sf.basedb.core.authentication.LoginRequest

Set the password to use.

setPassword(String) - Method in class net.sf.basedb.core.data.FileServerData

setPassword(String) - Method in class net.sf.basedb.core.FileServer

Set the password to use when authenticating with the file server.

setPassword(String) - Method in class net.sf.basedb.core.User

Set the password.

setPassword(String) - Method in class net.sf.basedb.util.uri.ConnectionParameters

setPassword(String) - Method in interface net.sf.basedb.util.zip.FilePacker

Set the password to use for encrypting the archive.

setPassword(String) - Method in class net.sf.basedb.util.zip.ZipFilePacker

setPassword(PasswordData) - Method in class net.sf.basedb.core.data.UserData

setPasswordField(FieldInfo) - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean

setPause(String, String, Serializable) - Method in interface net.sf.basedb.core.plugin.Response

A plug-in can call this method to notify the core that it has been paused.

setPause(String, String, Serializable) - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl

setPause(String, String, Serializable) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper

setPercentComplete(int) - Method in class net.sf.basedb.core.data.JobData

setPermanentEntityParameter(String, BasicItem) - Method in class net.sf.basedb.core.AbstractHqlQuery

setPermanentEntityParameter(String, BasicItem) - Method in interface net.sf.basedb.core.query.HqlQuery

Permanently set the value of an entity parameter.

setPermanentParameter(String, Object, Type) - Method in class net.sf.basedb.core.AbstractQuery

setPermanentParameter(String, Object, Type) - Method in interface net.sf.basedb.core.query.Query

Permanently set the value of a query parameter.

setPermission(int) - Method in class net.sf.basedb.core.data.keyring.KeyPermission

Set the permission.

setPermission(int) - Method in class net.sf.basedb.core.data.keyring.ProjectPermission

Set the permission.

setPermissions - Variable in class net.sf.basedb.plugins.PluginConfigurationImporter

setPermissions(Map<RoleKeyData, PluginPermission>) - Method in class net.sf.basedb.core.data.PluginDefinitionData

setPermissions(Group, Set<Permission>) - Method in class net.sf.basedb.core.GroupPermissions

Grant permissions to a group.

setPermissions(Group, Set<Permission>) - Method in class net.sf.basedb.core.MultiPermissions

Grant permissions to a group.

setPermissions(Group, Set<Permission>) - Method in class net.sf.basedb.core.Project

Grant a group permissions to this project.

setPermissions(Item, int, ItemKeyData, ProjectKeyData) - Static method in class net.sf.basedb.core.Install

setPermissions(Project, Set<Permission>) - Method in class net.sf.basedb.core.MultiPermissions

Grant permissions to a project.

setPermissions(Project, Set<Permission>) - Method in class net.sf.basedb.core.ProjectPermissions

Grant permissions to a project.

setPermissions(RoleKey, Set<Permission>, Set<Permission>) - Method in class net.sf.basedb.core.PluginDefinition

Sets the permissions for this plugin.

setPermissions(Role, Set<Permission>) - Method in class net.sf.basedb.core.RoleKey

Grant permissions to a role.

setPermissions(User, Set<Permission>) - Method in class net.sf.basedb.core.MultiPermissions

Grant permissions to a user.

setPermissions(User, Set<Permission>) - Method in class net.sf.basedb.core.Project

Grant a user permissions to this project.

setPermissions(User, Set<Permission>) - Method in class net.sf.basedb.core.UserPermissions

Grant permissions to a user.

setPermissionsParameter - Static variable in class net.sf.basedb.plugins.PluginConfigurationImporter

setPermissionTemplate(PermissionTemplateData) - Method in class net.sf.basedb.core.data.ProjectData

setPermissionTemplate(PermissionTemplate) - Method in class net.sf.basedb.core.Project

Set the permission template that should be used to share new items when this project is active.

setPhone(String) - Method in class net.sf.basedb.core.authentication.ExtraUserInformation

setPhone(String) - Method in class net.sf.basedb.core.data.UserData

setPhone(String) - Method in class net.sf.basedb.core.User

Set the phone number to the user, or null if unknown.

setPhysicalBioAssay(PhysicalBioAssayData) - Method in class net.sf.basedb.core.data.ArraySlideData

setPhysicalBioAssay(PhysicalBioAssayData) - Method in class net.sf.basedb.core.data.BioMaterialEventData

setPhysicalBioAssay(PhysicalBioAssay) - Method in class net.sf.basedb.core.BioMaterialEvent

Set the hybidization that was created by this event.

setPhysicalBioAssays(Set<PhysicalBioAssayData>) - Method in class net.sf.basedb.core.data.DerivedBioAssayData

setPlaceHolder(String) - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo

setPlate(int) - Method in class net.sf.basedb.core.data.MappingCoordinate

Set the plate number.

setPlate(PlateData) - Method in class net.sf.basedb.core.data.ArrayDesignPlateData

setPlate(PlateData) - Method in class net.sf.basedb.core.data.PlateEventData

setPlate(PlateData) - Method in class net.sf.basedb.core.data.WellData

setPlate(Plate) - Method in class net.sf.basedb.core.PlateEvent

Set the plate owning this event.

setPlateEvents(Set<PlateEventData>) - Method in class net.sf.basedb.core.data.PlateEventTypeData

setPlateEventType(PlateEventTypeData) - Method in class net.sf.basedb.core.data.PlateEventData

setPlateEventType(PlateEventType) - Method in class net.sf.basedb.core.PlateEvent

Set the plate event type of this event.

setPlateGeometry(PlateGeometryData) - Method in class net.sf.basedb.core.data.BioPlateData

setPlateGeometry(PlateGeometryData) - Method in class net.sf.basedb.core.data.PlateTypeData

setPlateGeometry(PlateGeometry) - Method in class net.sf.basedb.core.BioPlate

setPlateGeometry(PlateGeometry) - Method in class net.sf.basedb.core.PlateType

Set the plate geometry of this plate type.

setPlateList(List<Plate>) - Method in class net.sf.basedb.core.ArrayDesign

Set the list of plates to be used by this array design.

setPlateMapping(PlateMappingData) - Method in class net.sf.basedb.core.data.PlateData

setPlates(Set<ArrayDesignPlateData>) - Method in class net.sf.basedb.core.data.ArrayDesignData

setPlates(Set<PlateData>) - Method in class net.sf.basedb.core.data.PlateTypeData

setPlateType(PlateTypeData) - Method in class net.sf.basedb.core.data.PlateData

setPlateType(PlateTypeData) - Method in class net.sf.basedb.core.data.PlateEventTypeData

setPlateType(PlateType) - Method in class net.sf.basedb.core.Plate

Set the plate type of this plate.

setPlateType(PlateType) - Method in class net.sf.basedb.core.PlateEventType

Set the plate type owning this event type.

setPlateTypes(Set<PlateTypeData>) - Method in class net.sf.basedb.core.data.PlateGeometryData

setPlatform(PlatformData) - Method in class net.sf.basedb.core.data.ArrayDesignData

setPlatform(PlatformData) - Method in class net.sf.basedb.core.data.PlatformFileTypeData

setPlatform(PlatformData) - Method in class net.sf.basedb.core.data.PlatformVariantData

setPlatform(PlatformData) - Method in class net.sf.basedb.core.data.RawBioAssayData

setPlatform(Platform) - Method in class net.sf.basedb.core.ArrayDesign

Set the platform of the array design.

setPlatform(Platform) - Method in class net.sf.basedb.core.PlatformVariant

setPlatform(Platform, RawDataType) - Method in class net.sf.basedb.core.RawBioAssay

Set the platform and raw data type of the raw bioassay.

setPlatforms(Set<PlatformFileTypeData>) - Method in class net.sf.basedb.core.data.DataFileTypeData

setPlotGenerators(PlotGenerator[]) - Method in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean

setPlotServler(String) - Method in class net.sf.basedb.clients.web.extensions.plot.MAPlotFactory

setPlugin(PluginDefinitionData) - Method in class net.sf.basedb.core.data.ChangeHistoryData

setPluginConfiguration(PluginConfigurationData) - Method in class net.sf.basedb.core.data.JobData

setPluginConfiguration(PluginConfiguration) - Method in class net.sf.basedb.core.Job

Set the plugin configuration of this job.

setPluginDefinition(PluginDefinitionData) - Method in class net.sf.basedb.core.data.JobAgentSettingsData

setPluginDefinition(PluginDefinitionData) - Method in class net.sf.basedb.core.data.JobData

setPluginDefinition(PluginDefinitionData) - Method in class net.sf.basedb.core.data.PluginConfigurationData

setPluginDefinition(PluginDefinition) - Method in class net.sf.basedb.core.Job

Set the plugin configuration of this job.

setPluginDefinition(PluginDefinition) - Method in class net.sf.basedb.core.JobAgentSettings

setPluginDefinition(PluginDefinition) - Method in class net.sf.basedb.core.PluginConfiguration

The definition cannot be changed.

setPluginDefinitionId(int) - Method in class net.sf.basedb.core.data.keyring.PluginKeys

Sets the PluginDefinition:s ID

setPluginId(Integer) - Method in class net.sf.basedb.core.data.ChangeHistoryData

setPlugins(Map<PluginDefinitionData, JobAgentSettingsData>) - Method in class net.sf.basedb.core.data.JobAgentData

setPlugins(Set<PluginDefinitionData>) - Method in class net.sf.basedb.core.data.PluginTypeData

setPluginTypes(Set<PluginTypeData>) - Method in class net.sf.basedb.core.data.PluginDefinitionData

setPluginVersion(String) - Method in class net.sf.basedb.core.data.JobData

setPluginVersion(String) - Method in class net.sf.basedb.core.Job

Set the version of the plugin that executes the job.

setPort(Integer) - Method in class net.sf.basedb.core.data.JobAgentData

setPort(Integer) - Method in class net.sf.basedb.core.JobAgent

Set the port the job agent is listening on.

setPosition(int) - Method in class net.sf.basedb.core.BioMaterialEventSource

setPosition(int) - Method in class net.sf.basedb.core.data.ArrayDesignPlateData

setPosition(int) - Method in class net.sf.basedb.core.data.BioMaterialEventSourceData

setPosition(int) - Method in class net.sf.basedb.core.data.FeatureData

This method was private until 2.6.

setPosition(int) - Method in class net.sf.basedb.core.data.RawData

This method was private before 2.6.

setPosition(String) - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl

setPosition(String) - Method in class net.sf.basedb.core.BioPlate

Set the position within the "storage location" for this bioplate.

setPosition(String) - Method in class net.sf.basedb.core.data.BioPlateData

setPositionIndex(int) - Method in class net.sf.basedb.clients.web.ExperimentExplorer

Set the index of the curren position.

setPositionIndex(int) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo

Set the column index of the 'position' data column.

setPrefix(String) - Method in class net.sf.basedb.clients.web.taglib.table.CellValue

setPrefix(String) - Method in class net.sf.basedb.util.bfs.SequenceFilenameGenerator

Set the prefix that is used for file name generation.

setPrefixAndSuffix(String, String) - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerUtil

Sets a prefix and suffix string to use before and after the list of actions.

setPrepared(String, JobAgent) - Method in class net.sf.basedb.core.Job

Set the job's status to Job.Status.PREPARED.

setPrintRobot(HardwareData) - Method in class net.sf.basedb.core.data.ArrayBatchData

setPrintRobot(Hardware) - Method in class net.sf.basedb.core.ArrayBatch

Set the print robot used for this array batch.

setPriority(int) - Method in class net.sf.basedb.core.data.JobData

setPriority(int) - Method in class net.sf.basedb.core.Job

Set the priority of the job.

setPriorityBoost(int) - Method in class net.sf.basedb.core.data.JobAgentSettingsData

setPriorityBoost(int) - Method in class net.sf.basedb.core.JobAgentSettings

Set the priority boost given to jobs executed by this plugin.

setProducts(Set<BioAssaySetData>) - Method in class net.sf.basedb.core.data.TransformationData

setProgress(int, String) - Method in class net.sf.basedb.core.Job

Set the progress of the job.

setProgress(int, String) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

Update the progress of the export.

setProgress(int, String) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter

Update the progress of the export.

setProgress(int, String) - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter

Update the progress of the export.

setProgress(long, String) - Method in class net.sf.basedb.util.basefile.BaseFileParser

Update the progress of the parsing.

setProgressReporter(AbsoluteProgressReporter) - Method in class net.sf.basedb.util.basefile.BaseFileParser

Set a progress reporter that will be used to report how the parsing is progressing.

setProgressReporter(Job.ProgressReporterImpl) - Method in class net.sf.basedb.core.PluginConfigurationRequest

setProgressReporter(Job.ProgressReporterImpl) - Method in class net.sf.basedb.core.PluginExecutionRequest

Initialise a progress reporter that the plugin can use to store progress information in the database.

setProgressReporter(ProgressReporter) - Method in class net.sf.basedb.util.annotations.RunnableInheritAnnotationsManager

Set the progress reporter to use for reporting progress.

setProgressReporter(ProgressReporter) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

Set the progress reporter that is used to report progress.

setProgressReporter(ProgressReporter) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter

Set the progress reporter that is used to report progress.

setProgressReporter(ProgressReporter) - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter

Set the progress reporter that is used to report progress.

setProject(ProjectData) - Method in class net.sf.basedb.core.data.ChangeHistoryData

setProject(Project) - Method in class net.sf.basedb.core.FastAnnotationLoader

If the annotation type supports project-specific annotations this method can be used to control which values that are loaded.

setProject(Project) - Method in class net.sf.basedb.core.snapshot.SnapshotManager

When a project is set, the snapshot manager will only search for project-specific annotations explicitely belonging to that project (or default values if project == null).

setProjectAnnotations(boolean) - Method in class net.sf.basedb.core.AnnotationType

If this flag is set, annotation values can be set per project.

setProjectAnnotations(boolean) - Method in class net.sf.basedb.core.data.AnnotationTypeData

setProjectDefaults(Map<String, String>) - Method in class net.sf.basedb.core.data.ProjectData

setProjectDefaults(Project) - Method in class net.sf.basedb.core.ArrayBatch

Set print robot and protocol from project default settings.

setProjectDefaults(Project) - Method in class net.sf.basedb.core.BasicItem

This method is called before inserting new items into the database to allow items to propagate default values from the active project.

setProjectDefaults(Project) - Method in class net.sf.basedb.core.BioMaterialEvent

Set protocol and hardware from project default settings.

setProjectDefaults(Project) - Method in class net.sf.basedb.core.DerivedBioAssay

Set protocol, hardware and software from project default settings.

setProjectDefaults(Project) - Method in class net.sf.basedb.core.RawBioAssay

Set software, protocol and array design from project default settings.

setProjectId(int) - Method in class net.sf.basedb.core.Annotation

Set the project that this annotation value should belong to.

setProjectId(int) - Method in class net.sf.basedb.core.data.AnnotationData

setProjectId(int) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink

setProjectId(int) - Method in class net.sf.basedb.core.data.keyring.ProjectKeys

Set the id of the project.

setProjectId(int) - Method in class net.sf.basedb.core.data.keyring.ProjectPermission

Set the id of the project.

setProjectId(Integer) - Method in class net.sf.basedb.core.data.ChangeHistoryData

setProjectKey(ProjectKeyData) - Method in interface net.sf.basedb.core.data.ShareableData

Set the ProjectKeyData for the item.

setProjectKey(ProjectKeyData) - Method in class net.sf.basedb.core.data.SharedData

setProjectKey(ShareableData, ProjectKey) - Static method in class net.sf.basedb.core.ShareableUtil

Set the project key of a ShareableData object.

setProjectKey(ProjectKey) - Method in interface net.sf.basedb.core.Shareable

Set the ProjectKey for this item.

setProjectKey(ProjectKey) - Method in class net.sf.basedb.core.SharedItem

setProjectKeys(Set<ProjectKeyData>) - Method in class net.sf.basedb.core.data.ProjectData

setProjects(Map<ProjectData, Integer>) - Method in class net.sf.basedb.core.data.ProjectKeyData

setProjects(Set<ProjectData>) - Method in class net.sf.basedb.core.data.GroupData

setProjects(Set<ProjectData>) - Method in class net.sf.basedb.core.data.PermissionTemplateData

setProjects(Set<ProjectData>) - Method in class net.sf.basedb.core.data.UserData

setPrompt(String) - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo

setProperties(Object) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setProperties(Object) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setProperties(Map) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setProperties(Map) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setProperties(Map<String, ReporterClonePropertyData>) - Method in class net.sf.basedb.core.data.ReporterCloneTemplateData

setProperty(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

setProperty(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

setProperty(String) - Method in class net.sf.basedb.clients.web.taglib.PropertyValue

setProperty(String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

setProperty(String) - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField

Set the property that should be exported.

setProperty(String, Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

setProperty(String, String) - Static method in class net.sf.basedb.core.Config

Programatically set a configuration property that overrides a configuration setting in the base.config file.

setProperty(String, String) - Method in class net.sf.basedb.util.extensions.xml.PluginInfo

setPropertyFilter(PropertyFilter) - Method in class net.sf.basedb.core.ItemContext

Set a property filter.

setPropertyFilters(Map<String, PropertyFilterData>) - Method in class net.sf.basedb.core.data.ContextData

setPropertyFilters(Map<String, PropertyFilterData>) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData

setPropertyInspector(Filter<String>) - Method in class net.sf.basedb.core.ItemContext

Set a filter for this context that is used to inspect which properties that are allowed to be used in queries.

setPropertyValue(D, String, Object) - Method in class net.sf.basedb.core.BasicBatcher

Set a protected property value on a data object using Hibernate built-in reflection methods.

setProtocol(ProtocolData) - Method in class net.sf.basedb.core.data.ArrayBatchData

setProtocol(ProtocolData) - Method in class net.sf.basedb.core.data.BioMaterialEventData

setProtocol(ProtocolData) - Method in class net.sf.basedb.core.data.BioPlateEventData

setProtocol(ProtocolData) - Method in class net.sf.basedb.core.data.DerivedBioAssayData

setProtocol(ProtocolData) - Method in class net.sf.basedb.core.data.PlateEventData

setProtocol(ProtocolData) - Method in class net.sf.basedb.core.data.RawBioAssayData

setProtocol(Protocol) - Method in class net.sf.basedb.core.ArrayBatch

Set the Protocol used for printing the arrays.

setProtocol(Protocol) - Method in class net.sf.basedb.core.BioMaterialEvent

Set the Protocol that describes the procedure used in this event.

setProtocol(Protocol) - Method in class net.sf.basedb.core.BioPlateEvent

Set the Protocol that describes the procedure used in this event.

setProtocol(Protocol) - Method in class net.sf.basedb.core.DerivedBioAssay

Set the Protocol that describes the procedure used when creating this bioassay set.

setProtocol(Protocol) - Method in class net.sf.basedb.core.PlateEvent

Set the protocol that was followed in this event.

setProtocol(Protocol) - Method in class net.sf.basedb.core.RawBioAssay

Set the Protocol used while analysing the scanned images.

setProtocolParameter(boolean) - Method in class net.sf.basedb.core.AnnotationType

Specify if this annotation type should be used as a protocol parameter or as a regular annotation type

setProtocolParameter(boolean) - Method in class net.sf.basedb.core.data.AnnotationTypeData

setProtocols(Set<ProtocolData>) - Method in class net.sf.basedb.core.data.AnnotationTypeData

setProtocolType(ItemSubtypeData) - Method in class net.sf.basedb.core.data.PlateEventTypeData

setProtocolType(ItemSubtype) - Method in class net.sf.basedb.core.PlateEventType

Set the protocol type of this PlateTypeEvent item.

setPublic(boolean) - Method in class net.sf.basedb.core.data.ContextData

setPublication(String) - Method in class net.sf.basedb.core.data.ExperimentData

setPublication(String) - Method in class net.sf.basedb.core.Experiment

Set publication text.

setPublicationDate(Date) - Method in class net.sf.basedb.core.data.ExperimentData

setPublicationDate(Date) - Method in class net.sf.basedb.core.Experiment

Set the date this experiment was published.

setPubMedId(String) - Method in class net.sf.basedb.core.data.ExperimentData

setPubMedId(String) - Method in class net.sf.basedb.core.Experiment

Set the PubMed ID of the publication.

setPushAnnotations(boolean) - Method in class net.sf.basedb.core.data.ItemSubtypeData

setPushAnnotations(boolean) - Method in class net.sf.basedb.core.ItemSubtype

setQuantity(QuantityData) - Method in class net.sf.basedb.core.data.AnnotationTypeData

setQuantity(QuantityData) - Method in class net.sf.basedb.core.data.UnitData

setQuantity(QuantityData) - Method in class net.sf.basedb.core.data.UnitSymbolData

setQuantity(Quantity) - Method in class net.sf.basedb.core.Unit

setQuery(Query) - Method in class net.sf.basedb.core.ItemContext

setQuota(QuotaData) - Method in class net.sf.basedb.core.data.GroupData

setQuota(QuotaData) - Method in class net.sf.basedb.core.data.UserData

setQuota(Quota) - Method in class net.sf.basedb.core.Group

Set the quota for the group.

setQuota(Quota) - Method in class net.sf.basedb.core.User

Set the quota for the user.

setQuotaGroup(GroupData) - Method in class net.sf.basedb.core.data.UserData

setQuotaGroup(Group) - Method in class net.sf.basedb.core.User

Set the group whose quota should be checked for disk consuming items.

setQuotaType(QuotaTypeData) - Method in class net.sf.basedb.core.data.DiskUsageData

setQuotaType(QuotaTypeData) - Method in class net.sf.basedb.core.data.QuotaIndex

setQuotaValue(QuotaType, Location, long) - Method in class net.sf.basedb.core.Quota

Set the quota for the specified type, location and size.

setQuotaValues(Set<QuotaIndex>) - Method in class net.sf.basedb.core.data.QuotaData

setRange(int, int) - Method in class net.sf.basedb.util.ChainedProgressReporter

Set the range to use for the percentage values.

setRawBioAssay(RawBioAssayData) - Method in class net.sf.basedb.core.data.RawData

setRawBioAssay(RawBioAssayData) - Method in class net.sf.basedb.core.data.RootRawBioAssayData

setRawBioAssays(Set<RawBioAssayData>) - Method in class net.sf.basedb.core.data.DerivedBioAssayData

setRawBioAssays(Set<RawBioAssayData>) - Method in class net.sf.basedb.core.data.ExperimentData

setRawBioAssays(Set<RawBioAssayData>) - Method in class net.sf.basedb.core.data.ExtractData

setRawBioAssays(Set<RawBioAssayData>) - Method in class net.sf.basedb.core.data.JobData

setRawData(RawData) - Method in class net.sf.basedb.util.jep.MeanFunction

Set a new raw data object that will be used the next time the JEP expression is evaluated.

setRawData(RawData) - Method in class net.sf.basedb.util.jep.RawFunction

Set a new raw data object that will be used the next time the JEP expression is evaluated.

setRawDataType(String) - Method in class net.sf.basedb.core.data.ExperimentData

setRawDataType(String) - Method in class net.sf.basedb.core.data.FormulaData

setRawDataType(String) - Method in class net.sf.basedb.core.data.ItemListData

setRawDataType(String) - Method in class net.sf.basedb.core.data.PlatformData

setRawDataType(String) - Method in class net.sf.basedb.core.data.PlatformVariantData

setRawDataType(String) - Method in class net.sf.basedb.core.data.RawBioAssayData

setRawDataType(RawDataType) - Method in class net.sf.basedb.core.Experiment

Set the raw data type.

setRawDataType(RawDataType) - Method in class net.sf.basedb.core.Formula

Set the raw data type this formula can be used on.

setRawDataType(RawDataType) - Method in class net.sf.basedb.core.ItemList

Set the raw data type of raw bioassays that can be members in this list.

setRawDataType(RawDataType) - Method in class net.sf.basedb.core.Platform

Set the raw data type.

setRawDataType(RawDataType) - Method in class net.sf.basedb.core.PlatformVariant

Set the raw data type.

setRawParents(Set<RawBioAssayData>) - Method in class net.sf.basedb.core.data.BioAssayData

setRawSources(Collection<RawBioAssay>) - Method in class net.sf.basedb.core.Transformation

Set the raw bioassay sources used in this transformation.

setRawSources(Set<RawBioAssayData>) - Method in class net.sf.basedb.core.data.TransformationData

setRead(boolean) - Method in class net.sf.basedb.core.data.MessageData

setRead(boolean) - Method in class net.sf.basedb.core.Message

Set read status of the message.

setReadOnly(boolean) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setReadOnly(boolean) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setReadOnly(Object, boolean) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

setRecent(String, String, int) - Method in class net.sf.basedb.core.ItemContext

Add a value to the list of recently used values for the specified key.

setRecent(String, List<String>) - Method in class net.sf.basedb.core.ItemContext

setRecent(List<? extends BasicItem>) - Method in class net.sf.basedb.clients.web.taglib.Select

setRecent(BasicItem, int) - Method in class net.sf.basedb.core.ItemContext

Deprecated.

In 3.15, use ItemContext.setRecent(Item, BasicItem, int) which support 'null' entries

setRecent(BasicItem, String, int) - Method in class net.sf.basedb.core.ItemContext

Deprecated.

In 3.15, use ItemContext.setRecent(Item, BasicItem, String, int) which support 'null' entries

setRecent(BasicItem, ItemSubtype, int) - Method in class net.sf.basedb.core.ItemContext

Deprecated.

In 3.15, use ItemContext.setRecent(Item, BasicItem, ItemSubtype, int) which support 'null' entries

setRecent(Item, BasicItem, int) - Method in class net.sf.basedb.core.ItemContext

Add an item to the "recently used items" list.

setRecent(Item, BasicItem, String, int) - Method in class net.sf.basedb.core.ItemContext

Add an item to the "recently used items" list.

setRecent(Item, BasicItem, ItemSubtype, int) - Method in class net.sf.basedb.core.ItemContext

Add an item to the "recently used items" list when used for a specific item subtype.

setRedefinedColumnName(String, String, String) - Method in class net.sf.basedb.util.basefile.BaseFileParser

Redefined a column name for a specified section.

setReferenceFactor(double) - Method in class net.sf.basedb.core.data.UnitData

setReferenceOffset(double) - Method in class net.sf.basedb.core.data.UnitData

setReferenceUnit(String) - Method in class net.sf.basedb.core.data.QuantityData

setReferenceUnit(String) - Method in class net.sf.basedb.core.Quantity

Sets the reference unit.

setRegion(String) - Method in class net.sf.basedb.util.GeoLocation

setRelatedSubtype(ItemSubtype) - Method in class net.sf.basedb.core.ItemSubtype

Set a subtype that is related to this subtype.

setRelatedSubtypes(Map<Integer, ItemSubtypeData>) - Method in class net.sf.basedb.core.data.ItemSubtypeData

setReload(boolean) - Method in class net.sf.basedb.core.Keyring

setRemainingQuantity(Float) - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData

setRemember(boolean) - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl

setRememberLast(String) - Method in class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory

Set a flag indicating if errors should be remembered by the registry.

setRememberLastLogin(boolean) - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean

setRemoteId(String) - Method in class net.sf.basedb.core.data.SessionData

setRemove(boolean) - Method in class net.sf.basedb.util.annotations.InheritSpecification

Set a flag to remove all inherited annotations of the specified annotation type.

setRemoved(boolean) - Method in class net.sf.basedb.core.BioAssaySet

setRemoved(boolean) - Method in class net.sf.basedb.core.BioPlateEventType

setRemoved(boolean) - Method in class net.sf.basedb.core.BioPlateType

setRemoved(boolean) - Method in class net.sf.basedb.core.CommonItem

setRemoved(boolean) - Method in class net.sf.basedb.core.DataFileType

setRemoved(boolean) - Method in class net.sf.basedb.core.Directory

setRemoved(boolean) - Method in class net.sf.basedb.core.ExtraValueType

setRemoved(boolean) - Method in class net.sf.basedb.core.Group

setRemoved(boolean) - Method in class net.sf.basedb.core.ItemSubtype

setRemoved(boolean) - Method in class net.sf.basedb.core.Message

setRemoved(boolean) - Method in class net.sf.basedb.core.MimeType

setRemoved(boolean) - Method in class net.sf.basedb.core.News

setRemoved(boolean) - Method in class net.sf.basedb.core.PlateEventType

setRemoved(boolean) - Method in class net.sf.basedb.core.PlateGeometry

setRemoved(boolean) - Method in class net.sf.basedb.core.Platform

setRemoved(boolean) - Method in class net.sf.basedb.core.PlatformVariant

setRemoved(boolean) - Method in class net.sf.basedb.core.PluginDefinition

setRemoved(boolean) - Method in class net.sf.basedb.core.PluginType

setRemoved(boolean) - Method in class net.sf.basedb.core.Project

setRemoved(boolean) - Method in class net.sf.basedb.core.Quantity

setRemoved(boolean) - Method in class net.sf.basedb.core.Quota

setRemoved(boolean) - Method in interface net.sf.basedb.core.Removable

Set the removed flag for this item.

setRemoved(boolean) - Method in class net.sf.basedb.core.ReporterType

setRemoved(boolean) - Method in class net.sf.basedb.core.Role

setRemoved(boolean) - Method in class net.sf.basedb.core.Transformation

setRemoved(boolean) - Method in class net.sf.basedb.core.Unit

setRemoved(boolean) - Method in class net.sf.basedb.core.User

setRemoved(DbControl, Item, Set<Integer>, boolean) - Static method in class net.sf.basedb.util.RemovableUtil

setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.BioAssaySetData

setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.BioPlateEventTypeData

setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.BioPlateTypeData

setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.CommonData

setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.DataFileTypeData

setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.ExtraValueTypeData

setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.GroupData

setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.ItemSubtypeData

setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.MessageData

setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.MimeTypeData

setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.NewsData

setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.PlateEventTypeData

setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.PlateGeometryData

setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.PlatformData

setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.PlatformVariantData

setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.PluginDefinitionData

setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.PluginTypeData

setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.ProjectData

setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.QuantityData

setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.QuotaData

setRemovedBy(Integer) - Method in interface net.sf.basedb.core.data.RemovableData

Set the ID of the user that removed this item or null to restore the item.

setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.ReporterTypeData

setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.RoleData

setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.TransformationData

setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.UnitData

setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.UserData

setRemovedFlag(Removable, boolean) - Static method in class net.sf.basedb.util.RemovableUtil

setRemoveJobWhenFinished(boolean) - Method in class net.sf.basedb.core.data.JobData

setRemoveJobWhenFinished(boolean) - Method in class net.sf.basedb.core.Job

Set if the job should be deleted after it has finished successfully.

setRenderer(Renderer<?>) - Method in class net.sf.basedb.clients.web.taglib.extensions.Render

setRendererFactory(RendererFactory<? super A>) - Method in class net.sf.basedb.util.extensions.ExtensionBean

setRendererFactory(RendererFactory<? super A>) - Method in class net.sf.basedb.util.extensions.ExtensionPointBean

setReplaceExisting(boolean) - Method in class net.sf.basedb.util.annotations.InheritSpecification

If this flag is set (default=false), existing inherited annotations of the specified annotation type are removed before inheriting new ones.

setReporter(ReporterData) - Method in class net.sf.basedb.core.data.FeatureData

setReporter(ReporterData) - Method in class net.sf.basedb.core.data.RawData

setReporter(ReporterData) - Method in class net.sf.basedb.core.data.ReporterListScoreData

setReporter(ReporterData) - Method in class net.sf.basedb.core.data.WellData

setReporter(ReporterData) - Method in class net.sf.basedb.core.Well

Set the reporter of this well.

setReporter(ReporterData) - Method in class net.sf.basedb.util.jep.ReporterFunction

Set a new reporter object that will be used the next time the JEP expression is evaluated.

setReporterAnnotationsWriter(AnnotationWriter) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter

Set the stream were reporter annotations should be written.

setReporterCloneTemplate(ReporterCloneTemplateData) - Method in class net.sf.basedb.core.data.VirtualDbData

setReporterId(int) - Method in class net.sf.basedb.core.data.ReporterListScoreData

setReporterIndex(int) - Method in class net.sf.basedb.clients.web.ExperimentExplorer

Set the index of the currently viewed reporter.

setReporterList(ReporterListData) - Method in class net.sf.basedb.core.data.ReporterListScoreData

setReporterLists(Set<ReporterListData>) - Method in class net.sf.basedb.core.data.ExperimentData

setReporterListScores(Map<Integer, ReporterListScoreData>) - Method in class net.sf.basedb.core.data.ReporterListData

setReporterListScores(Set<ReporterListScoreData>) - Method in class net.sf.basedb.core.data.ReporterData

setReporters(Set<ReporterData>) - Method in class net.sf.basedb.core.data.ReporterTypeData

This is the inverse end.

setReporterType(ReporterData, ReporterType) - Static method in class net.sf.basedb.core.Reporter

Set the reporter type on a reporter data object.

setReporterType(ReporterTypeData) - Method in class net.sf.basedb.core.data.ReporterData

setRequired(boolean) - Method in class net.sf.basedb.clients.web.taglib.Select

setRequired(boolean) - Method in class net.sf.basedb.core.data.ItemSubtypeFileTypeData

setRequired(boolean) - Method in class net.sf.basedb.core.data.PlatformFileTypeData

setRequired(boolean) - Method in class net.sf.basedb.core.ItemSubtypeFileType

Set the required flag for this file type.

setRequired(boolean) - Method in class net.sf.basedb.core.PlatformFileType

Set the required flag for this file type.

setRequired(boolean) - Method in class net.sf.basedb.plugins.executor.ParameterDefinition

Set if this parameter should be a required or optional parameter.

setRequiredForMiame(boolean) - Method in class net.sf.basedb.core.AnnotationType

Set if an annotation of this annotation type is required for an item to be compliant with the MIAME recommendation.

setRequiredForMiame(boolean) - Method in class net.sf.basedb.core.data.AnnotationTypeData

setRequiresConfiguration(boolean) - Method in class net.sf.basedb.core.data.PluginDefinitionData

setRequiresConfiguration(boolean) - Method in class net.sf.basedb.core.PluginDefinition

setResetClassLoader(boolean) - Method in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor

This flag controls if the class loader should be reset or not.

setResetErrorFlag(boolean) - Method in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor

This flag controls if the error flag should be reset or not.

setResponseFilter(Filter<HttpResponse>) - Method in class net.sf.basedb.util.uri.http.HttpConnectionManager

Set a filter that will inspect the response before an input stream is returned to the calling code.

setRestrictionParameters(NativeQuery<?>) - Method in class net.sf.basedb.core.AnnotationBetweenRestriction

setRestrictionParameters(NativeQuery<?>) - Method in class net.sf.basedb.core.AnnotationInRestriction

setRestrictionParameters(NativeQuery<?>) - Method in class net.sf.basedb.core.AnnotationRestriction

Set the value for all parameters defined in the SQL fragment returned by AnnotationRestriction.getRestrictionSql(Query, DbControl).

setRestrictionParameters(NativeQuery<?>) - Method in class net.sf.basedb.core.AnnotationSimpleRestriction

setRestrictionParameters(NativeQuery<?>) - Method in class net.sf.basedb.core.HasAnnotationRestriction

setResult(boolean, String) - Method in class net.sf.basedb.util.fileset.ValidatingFileSetMember

Set the result of the validation for this file.

setResult(SqlResult, SqlResult) - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult

setResultIntensityTransform(Integer) - Method in class net.sf.basedb.core.data.FormulaData

setResultIntensityTransform(IntensityTransform) - Method in class net.sf.basedb.core.Formula

Sets the transform that this formula generates.

setResultSetMapping(String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setResultTransformer(ResultTransformer) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setResyncCloned(boolean) - Method in class net.sf.basedb.util.annotations.InheritSpecification

setReturnKeys(boolean) - Method in class net.sf.basedb.util.resources.ResourceBundleWrapper

Set a flag indicating that the various getString() methods should always return the key instead of trying to find a value for it.

setReturnTotalCount(boolean) - Method in class net.sf.basedb.core.AbstractQuery

setReturnTotalCount(boolean) - Method in interface net.sf.basedb.core.query.Query

Specify if the query should return a count for the total number of items that would have been returned if the Query.setFirstResult(int) and Query.setMaxResults(int) had been disabled, or if the results are loaded by an iterator where the number of rows not are known beforehand.

setRole(String) - Method in class net.sf.basedb.core.BioPlateEventParticipant

Set the role that the plate has in this event.

setRole(String) - Method in class net.sf.basedb.core.data.BioPlateEventParticipantData

setRoleId(int) - Method in class net.sf.basedb.core.data.keyring.RoleKeys

Set the id of the role.

setRoleId(int) - Method in class net.sf.basedb.core.data.keyring.UserRoles

Set the id of the role.

setRoleInactive(int, boolean) - Method in class net.sf.basedb.core.Keyring

Set a roles as inactive (or active).

setRoleInactive(int, boolean) - Method in class net.sf.basedb.core.SessionControl

Set a role as active or inactive.

setRoles(Map<RoleData, Integer>) - Method in class net.sf.basedb.core.data.RoleKeyData

setRoles(Set<RoleData>) - Method in class net.sf.basedb.core.data.UserData

setRoot(boolean) - Method in class net.sf.basedb.core.data.DerivedBioAssayData

setRoot(String) - Method in class net.sf.basedb.util.extensions.xml.PathConverter

Set the value of the root path.

setRootDerivedBioAssays(Set<DerivedBioAssayData>) - Method in class net.sf.basedb.core.data.PhysicalBioAssayData

setRootPath(String) - Method in class net.sf.basedb.core.data.FileServerData

setRootPath(String) - Method in class net.sf.basedb.core.FileServer

Set the root path that should be added to all URI:s when used with this file server.

setRootPath(String) - Method in class net.sf.basedb.util.uri.ConnectionParameters

setRootRawBioAssays(Map<RawBioAssayData, RootRawBioAssayData>) - Method in class net.sf.basedb.core.data.ExperimentData

setRow(int) - Method in class net.sf.basedb.clients.web.taglib.table.PropertyFilter

setRow(int) - Method in class net.sf.basedb.core.data.BioWellData

setRow(int) - Method in class net.sf.basedb.core.data.FeatureData

setRow(int) - Method in class net.sf.basedb.core.data.MappingCoordinate

Set the row number.

setRow(int) - Method in class net.sf.basedb.core.data.PlateCoordinate

Set the row number.

setRow(int) - Method in class net.sf.basedb.core.data.WellData

setRow(Integer) - Method in class net.sf.basedb.core.data.RawData

setRowIndex(int) - Method in class net.sf.basedb.core.PropertyFilter

Only used internally when removing filter rows

setRows(int) - Method in class net.sf.basedb.core.data.PlateGeometryData

setRows(int) - Method in class net.sf.basedb.core.PlateGeometry

The number of rows cannot be changed, used at object creation only.

setRowSeparator(String) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil

Set the row separator.

setRowsperpage(int) - Method in class net.sf.basedb.clients.web.taglib.table.Navigator

setRowsperpage(String) - Method in class net.sf.basedb.clients.web.taglib.table.Navigator

setRowsPerPage(int) - Method in class net.sf.basedb.core.data.ContextData

setRowsPerPage(int) - Method in class net.sf.basedb.core.ItemContext

Set the number of rows the current table page should show.

setSafeResources(String, boolean) - Static method in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter

Set a flag indicating if resources from the given extension JAR file are should use the regular policy or the 'unsafe-resources' policy.

setSampleSize(int) - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics

setSc(SessionControl) - Method in class net.sf.basedb.clients.web.taglib.Page

Set the session control to use in this request.

setSc(SessionControl) - Method in class net.sf.basedb.clients.web.taglib.table.Table

setScheduled(String, JobAgent) - Method in class net.sf.basedb.core.Job

Set the job's status to Job.Status.WAITING.

setScheduled(Date) - Method in class net.sf.basedb.core.data.JobData

setSchemaVersion(int) - Method in class net.sf.basedb.core.data.SchemaVersionData

setSchemaVersion(String, int) - Method in class net.sf.basedb.core.hibernate.SessionFactoryConfiguration

Deprecated.

Set the schema version of the current configuration.

setSchemaVersion(Session, int) - Static method in class net.sf.basedb.core.Update

setSchemaVersion(Session, String, int, int) - Static method in class net.sf.basedb.core.Update

Update the database with a new schema version number.

setSchemaVersionInTransaction(Session, int) - Static method in class net.sf.basedb.core.Update

Update the schema version version number using a new transaction.

setScore(Float) - Method in class net.sf.basedb.core.data.ReporterListScoreData

setScript(String) - Method in class net.sf.basedb.clients.web.extensions.AbstractJspFactory

Add a reference to a javascript file to the factory.

setScripts(String) - Method in class net.sf.basedb.clients.web.taglib.Head

setSection(String) - Method in class net.sf.basedb.core.BioPlate

Set the section within the "storage location" for this bioplate.

setSection(String) - Method in class net.sf.basedb.core.data.BioPlateData

setSectionParser(String, BaseFileSectionParser) - Method in class net.sf.basedb.util.basefile.BaseFileParser

Adds a section parser.

setSectionRegexp(Pattern) - Method in class net.sf.basedb.util.parser.FlatFileParser

Set a regular expression that can be matched against the section line.

setSelectdefault(boolean) - Method in class net.sf.basedb.clients.web.taglib.Select

setSelectrecent(boolean) - Method in class net.sf.basedb.clients.web.taglib.Select

setSender(UserData) - Method in class net.sf.basedb.core.Message

setSendMessage(boolean) - Method in class net.sf.basedb.core.data.JobData

setSendMessage(boolean) - Method in class net.sf.basedb.core.Job

Set if a message should be sent to owner when the job finishes.

setSendMessagesAsEmail(boolean) - Method in class net.sf.basedb.core.data.UserData

setSendMessagesAsEmail(boolean) - Method in class net.sf.basedb.core.User

Set a flag indicating that all messages should also be sent as email.

setSeparator(String) - Method in class net.sf.basedb.clients.web.taglib.table.CellValue

setSerializable(int, Serializable) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setSerializable(String, Serializable) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setServer(String) - Method in class net.sf.basedb.core.data.JobAgentData

setServer(String) - Method in class net.sf.basedb.core.data.JobData

setServer(String) - Method in class net.sf.basedb.core.JobAgent

Set the name/IP of the server where the job agent is running.

setServerCertificate(byte[]) - Method in class net.sf.basedb.core.data.FileServerData

setServerCertificate(byte[]) - Method in class net.sf.basedb.core.FileServer

Set the public server certificate so that BASE can trust https connections to the server.

setServerCertificate(byte[]) - Method in class net.sf.basedb.util.uri.ConnectionParameters

setServletContext(ServletContext) - Method in class net.sf.basedb.clients.web.extensions.ServletWrapper

Set the servlet context from the web application.

setSession(SessionData) - Method in class net.sf.basedb.core.data.ChangeHistoryData

setSessionId(int) - Method in class net.sf.basedb.core.data.ChangeHistoryData

setSessions(Set<SessionData>) - Method in class net.sf.basedb.core.data.ClientData

setSessions(Set<SessionData>) - Method in class net.sf.basedb.core.data.UserData

setSessions(Set<SessionData>) - Method in class net.sf.basedb.core.data.UserDeviceData

setSessionSetting(String, Object) - Method in class net.sf.basedb.core.SessionControl

Set the value of a session setting.

setSetting(String, String) - Method in class net.sf.basedb.core.ItemContext

Set a value.

setSetting(String, String) - Method in class net.sf.basedb.core.Presets.Preset

Set a value for the specified setting.

setSetting(String, String, String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Set a configuration setting for an extension.

setSetting(String, String, String) - Method in class net.sf.basedb.util.extensions.manager.Settings

Set a configuration setting for an extension.

setSettings(Map<String, String>) - Method in class net.sf.basedb.core.data.ContextData

setSeverity(ValidationRuleAction, Severity) - Method in class net.sf.basedb.util.overview.ValidationOptions

Set a severity level for the specified validation rule.

setShort(int, short) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setShort(String, short) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setShortName(String) - Method in class net.sf.basedb.core.AnnotationTypeCategory

Set the short name.

setShortName(String) - Method in class net.sf.basedb.core.data.AnnotationTypeCategoryData

setShow(String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

setShowclazz(String) - Method in class net.sf.basedb.clients.web.taglib.HideableSection

setShowClazz(String) - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory

setShowClazz(String) - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean

setSignalReceiver(SignalReceiver) - Method in class net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor

setSignalTransporter(Class<? extends SignalTransporter>, String) - Method in class net.sf.basedb.core.Job

Set information needed to create a signal transporter object that can be used to send signals to the plug-in that is currently executing this job.

setSignalTransporter(String) - Method in class net.sf.basedb.core.data.JobData

setSize(int) - Method in class net.sf.basedb.core.data.ItemListData

setSize(int) - Method in class net.sf.basedb.core.data.PhysicalBioAssayData

setSize(int) - Method in class net.sf.basedb.core.data.ReporterListData

setSize(int) - Method in class net.sf.basedb.core.PhysicalBioAssay

Set the size of the bioassay.

setSize(long) - Method in class net.sf.basedb.core.data.FileData

setSizeAtLastSync(int) - Method in class net.sf.basedb.core.data.ItemListData

setSkip(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Hidden

setSmartenum(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

setSnapshotInvalid() - Method in class net.sf.basedb.core.AnnotationSet

Mark the snapshot (if it exists) of this annotation set as invalid.

setSnapshotManager(SnapshotManager) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

Set's the snapshot manager that should be used to load annotation values.

setSnapshotManager(SnapshotManager) - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter

Set a snapshot manager that should be used with annotation-based fields.

setSnapshotManager(SnapshotManager) - Method in class net.sf.basedb.util.export.spotdata.AnnotationAssayField

Set the snapshot manager that should be used to load annotation values.

setSoftware(SoftwareData) - Method in class net.sf.basedb.core.data.DerivedBioAssayData

setSoftware(SoftwareData) - Method in class net.sf.basedb.core.data.RawBioAssayData

setSoftware(Software) - Method in class net.sf.basedb.core.DerivedBioAssay

Set the Software that was used when creating this bioassay set.

setSoftware(Software) - Method in class net.sf.basedb.core.RawBioAssay

Set the Software used while analysing the scanned images.

setSortable(boolean) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

setSortable(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

setSortable(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

setSortby(String) - Method in class net.sf.basedb.clients.web.taglib.table.Table

setSortDirection(int) - Method in class net.sf.basedb.core.data.ContextData

setSortDirection(ItemContext.SortDirection) - Method in class net.sf.basedb.core.ItemContext

Set the sort direction (ascending or descending) of the current listing.

setSortproperty(String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

setSortProperty(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

setSortProperty(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

setSortProperty(String) - Method in class net.sf.basedb.core.data.ContextData

setSortProperty(String) - Method in class net.sf.basedb.core.ItemContext

Set the name of the property that the current listing is sorted by.

setSource(int) - Method in class net.sf.basedb.core.data.AnnotationData

setSource(int) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink

setSource(BioAssaySet) - Method in class net.sf.basedb.core.Transformation

Set the source bioassayset.

setSource(BioAssaySet) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

Set the bioassay set that is used as a source for the spot data.

setSource(BioMaterial) - Method in class net.sf.basedb.core.BioMaterialEvent

Set a single parent item for this event.

setSource(BioAssaySetData) - Method in class net.sf.basedb.core.data.TransformationData

setSourceCoordinate(MappingCoordinate, MappingCoordinate) - Method in class net.sf.basedb.core.PlateMapping

Set the source coordinate for a given destination coordinate.

setSourceCount(int) - Method in class net.sf.basedb.core.data.PlateMappingData

setSourceCount(int) - Method in class net.sf.basedb.core.PlateMapping

Set the number of source plates.

setSourceFileWrapper(FileWrapper) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter

Set the source BASEfile to import data from.

setSourceGeometry(PlateGeometryData) - Method in class net.sf.basedb.core.data.PlateMappingData

setSourceGeometry(PlateGeometry) - Method in class net.sf.basedb.core.PlateMapping

Set the source geometry.

setSourceIntensityTransform(Integer) - Method in class net.sf.basedb.core.data.FormulaData

setSourceIntensityTransform(IntensityTransform) - Method in class net.sf.basedb.core.Formula

Sets the transform that is required on spot data if this formula should generate the correct result.

setSourceItemMustExist(boolean) - Method in class net.sf.basedb.core.SyncFilter

setSourceItemTransform(int) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData

setSourceItemType(int) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData

setSourceMustExist(boolean) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData

setSources(Map<BioMaterialData, BioMaterialEventSourceData>) - Method in class net.sf.basedb.core.data.BioMaterialEventData

setSpacingX(int) - Method in class net.sf.basedb.core.ArrayDesignBlock

Set the x spacing between the spots in the slide.

setSpacingX(int) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData

setSpacingX(Integer) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock

setSpacingY(int) - Method in class net.sf.basedb.core.ArrayDesignBlock

Set the y spacing between the spots in the slide.

setSpacingY(int) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData

setSpacingY(Integer) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock

setSpecialLogger(Class<? extends LoggableData>, EntityLogger) - Method in class net.sf.basedb.core.log.db.DbLogManagerFactory

Register a special logger for entities of the given class.

setSpotIntensityParser(SpotIntensityParser) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo

Set the spot intensity parser for the section.

setSpots(int) - Method in class net.sf.basedb.core.data.RawBioAssayData

setSqlResult(SqlResult) - Method in class net.sf.basedb.util.jep.ChannelFunction

Set a new SqlResult object that will be used the next time the JEP expression is evaluated.

setSqlResult(SqlResult) - Method in class net.sf.basedb.util.jep.ExtraValueFunction

Set a new SqlResult object that will be used the next time the JEP expression is evaluated.

setSqlResult(SqlResult) - Method in class net.sf.basedb.util.jep.RawChannelFunction

Set a new SqlResult object that will be used the next time the JEP expression is evaluated.

setSqlResult(SqlResult) - Method in class net.sf.basedb.util.jep.ScoreFunction

Set a new SqlResult object that will be used the next time the JEP expression is evaluated.

setSshFingerprint(String) - Method in class net.sf.basedb.core.data.FileServerData

setSshFingerprint(String) - Method in class net.sf.basedb.core.FileServer

Set the SSH fingerprint for the server.

setSshFingerprint(String) - Method in class net.sf.basedb.util.uri.ConnectionParameters

setSshPrivateKey(byte[]) - Method in class net.sf.basedb.core.data.FileServerData

setSshPrivateKey(byte[]) - Method in class net.sf.basedb.core.FileServer

Set the private that BASE should use to authenticate with the server when connecting with SSH.

setSshPrivateKey(byte[]) - Method in class net.sf.basedb.util.uri.ConnectionParameters

setSshPrivateKeyFormat(String) - Method in class net.sf.basedb.core.data.FileServerData

setSshPrivateKeyFormat(String) - Method in class net.sf.basedb.core.FileServer

Set the format of the SSH private key.

setSshPrivateKeyFormat(String) - Method in class net.sf.basedb.util.uri.ConnectionParameters

setSshPrivateKeyPassword(String) - Method in class net.sf.basedb.core.data.FileServerData

setSshPrivateKeyPassword(String) - Method in class net.sf.basedb.core.FileServer

Set the password that is needed to unlock the SSH private key.

setSshPrivateKeyPassword(String) - Method in class net.sf.basedb.util.uri.ConnectionParameters

setStackTrace(String) - Method in class net.sf.basedb.core.data.JobData

setStartDate(Date) - Method in class net.sf.basedb.core.data.NewsData

setStartDate(Date) - Method in class net.sf.basedb.core.News

Set the start date and time for this item to be published.

setStarted(Class<? extends SignalTransporter>, String) - Method in class net.sf.basedb.core.Job.ProgressReporterImpl

setStarted(Date) - Method in class net.sf.basedb.core.data.JobData

setStatus(int) - Method in class net.sf.basedb.core.data.JobData

setStatus(ExtensionsFile, String) - Method in class net.sf.basedb.util.extensions.manager.ProcessResults

Sets a short overall status message for an entire file.

setStatusMessage(String) - Method in class net.sf.basedb.core.data.JobData

setSticky(boolean) - Method in class net.sf.basedb.core.data.NewsData

setSticky(boolean) - Method in class net.sf.basedb.core.News

Set the sticky flag for this news item.

setStickyheaders(String) - Method in class net.sf.basedb.clients.web.taglib.table.Table

setStorageType(ItemSubtypeData) - Method in class net.sf.basedb.core.data.BioPlateTypeData

setStorageType(ItemSubtype) - Method in class net.sf.basedb.core.BioPlateType

Set the subtype of storage location where plates of this type are usually stored.

setString(int, String) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setString(String, String) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setStringValues(List<String>) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink

setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo

setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean

setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

Set the style to use in all cases.

setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory

setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean

setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory

setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory

setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean

setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean

setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory

setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

Set the style to use in all cases.

setStyle(String) - Method in class net.sf.basedb.clients.web.taglib.StylableTag

setStyle(String) - Method in class net.sf.basedb.clients.web.taglib.tab.Tab

setStyle(String) - Method in class net.sf.basedb.clients.web.taglib.table.Cell

setStyle(String) - Method in class net.sf.basedb.clients.web.taglib.table.CellValue

setStyles(String) - Method in class net.sf.basedb.clients.web.taglib.Head

setStylesheet(String) - Method in class net.sf.basedb.clients.web.extensions.AbstractJspFactory

Add a reference to a CSS stylesheet file to the factory.

setSubCategories(Set<AnnotationTypeCategoryData>) - Method in class net.sf.basedb.core.data.ItemSubtypeData

setSubCategoriesAnnotationType(AnnotationType) - Method in class net.sf.basedb.core.ItemSubtype

Set an annotation type to use for dividing into sub-categories when mapping to annotation type categories.

setSubCategoriesAnnotationType(AnnotationTypeData) - Method in class net.sf.basedb.core.data.ItemSubtypeData

setSubcategory(AnnotationTypeCategory) - Method in class net.sf.basedb.clients.web.taglib.SubtypeSelector

setSubCategory(AnnotationTypeCategory, ItemContext.AddFilter) - Method in class net.sf.basedb.core.ItemContext

Set a sub-category to relate to this context.

setSubCategory(AnnotationTypeCategoryData) - Method in class net.sf.basedb.core.data.ContextData

setSubCategoryValues(List<?>) - Method in class net.sf.basedb.core.AnnotationTypeCategory

Set the list of values that should be used to match sub-categories.

setSubCategoryValues(ParameterValueData<?>) - Method in class net.sf.basedb.core.data.AnnotationTypeCategoryData

setSubclass(String) - Method in class net.sf.basedb.clients.web.taglib.StylableTag

setSubclass(String) - Method in class net.sf.basedb.clients.web.taglib.table.Cell

setSubcontext(String) - Method in class net.sf.basedb.clients.web.taglib.table.Table

setSubContext(String) - Method in class net.sf.basedb.core.data.ContextData

setSubContext(String) - Method in class net.sf.basedb.core.data.ContextIndex

setSubContext(String) - Method in class net.sf.basedb.core.data.JobData

setSubdirectories(Set<DirectoryData>) - Method in class net.sf.basedb.core.data.DirectoryData

setSubid(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu

setSubmenuId(String) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

setSubmenuId(String) - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean

setSubmenuId(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

setSubtitle(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

setSubtitle(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

setSubtitle(String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

setSubtype(String) - Method in class net.sf.basedb.util.bfs.MetadataModel

Set the subtype of the BFS.

setSubtype(String) - Method in class net.sf.basedb.util.bfs.MetadataWriter

Set the BFS subtype for this writer.

setSubtypes(List<ItemSubtype>) - Method in class net.sf.basedb.clients.web.taglib.SubtypeSelector

setSuffix(String) - Method in class net.sf.basedb.clients.web.taglib.table.CellValue

setSuffix(String) - Method in class net.sf.basedb.util.bfs.SequenceFilenameGenerator

Set the suffix that is used for file name generation.

setSuggestedJobName(String) - Method in interface net.sf.basedb.core.plugin.Response

A plug-in may call this method on it's job configuration phase to suggest a name for the job.

setSuggestedJobName(String) - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl

setSuggestedJobName(String) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper

setSummary(String) - Method in class net.sf.basedb.util.extensions.manager.ProcessResults

Set a summary of the results.

setSupportsConfigurations(boolean) - Method in class net.sf.basedb.core.data.PluginDefinitionData

setSupportsConfigurations(boolean) - Method in class net.sf.basedb.core.PluginDefinition

setSupportsDeviceVerification(boolean) - Method in class net.sf.basedb.core.Client

setSupportsDeviceVerification(boolean) - Method in class net.sf.basedb.core.data.ClientData

setSymbol(String) - Method in class net.sf.basedb.core.data.ReporterData

setSymbol(String) - Method in class net.sf.basedb.core.data.UnitSymbolData

setSymbols(Set<String>) - Method in class net.sf.basedb.core.Unit

Set the symbols that should be registered for this unit.

setSymbols(Set<UnitSymbolData>) - Method in class net.sf.basedb.core.data.QuantityData

setSymbols(Set<UnitSymbolData>) - Method in class net.sf.basedb.core.data.UnitData

setSyncContext(ItemContext, SyncFilter.SourceItemTransform) - Method in class net.sf.basedb.core.SyncFilter

Copy filters and other settings from the given context to this synchronization filter.

setSyncDate(Date) - Method in class net.sf.basedb.core.data.ItemListData

setSyncFilters(Set<ItemListSyncFilterData>) - Method in class net.sf.basedb.core.data.ItemListData

setSystemId(String) - Method in class net.sf.basedb.core.BioPlateEventType

setSystemId(String) - Method in class net.sf.basedb.core.data.BioPlateEventTypeData

setSystemId(String) - Method in class net.sf.basedb.core.data.DirectoryData

setSystemId(String) - Method in class net.sf.basedb.core.data.GroupData

setSystemId(String) - Method in class net.sf.basedb.core.data.ItemSubtypeData

setSystemId(String) - Method in class net.sf.basedb.core.data.QuantityData

setSystemId(String) - Method in class net.sf.basedb.core.data.QuotaData

setSystemId(String) - Method in class net.sf.basedb.core.data.QuotaTypeData

setSystemId(String) - Method in class net.sf.basedb.core.data.RoleData

setSystemId(String) - Method in class net.sf.basedb.core.data.UserData

setTabcontrol(String) - Method in class net.sf.basedb.clients.web.taglib.Help

setTabindex(int) - Method in class net.sf.basedb.clients.web.taglib.Button

setTabindex(int) - Method in class net.sf.basedb.clients.web.taglib.Help

setTabindex(int) - Method in class net.sf.basedb.clients.web.taglib.Icon

setTabindex(int) - Method in class net.sf.basedb.clients.web.taglib.Input

setTabindex(int) - Method in class net.sf.basedb.clients.web.taglib.Select

setTabindex(int) - Method in class net.sf.basedb.clients.web.taglib.tab.Tab

setTabindex(int) - Method in class net.sf.basedb.clients.web.taglib.table.Button

setTabindex(int) - Method in class net.sf.basedb.clients.web.taglib.Zoom

setTabIndex(int) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean

setTabIndex(int) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean

setTabIndex(int) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory

setTabIndex(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory

setTabIndex(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory

setTable(String) - Method in class net.sf.basedb.clients.web.taglib.SubtypeSelector

setTag(TagData) - Method in class net.sf.basedb.core.data.ExtractData

setTag(Tag) - Method in class net.sf.basedb.core.Extract

Set the tag that was applied to this extract in order to be able to distinguish it from other extracts on a physical bioassay.

setTarget(ScriptTargetOutput) - Method in class net.sf.basedb.core.hibernate.DbIndexWork

Set a target for receiving information about SQL statements that are needed to create missing foreign keys and indexes.

setTargetType(Item) - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics

setTemporary(boolean) - Method in class net.sf.basedb.core.PropertyFilter

Set or clear a flag indicating that this filter is temporary filter.

setText(int, String) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setText(String, String) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setTextarea(String) - Method in class net.sf.basedb.clients.web.taglib.CalendarButton

setTextarea(String) - Method in class net.sf.basedb.clients.web.taglib.Zoom

setTextValues(List<String>) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink

setTheId(int) - Method in class net.sf.basedb.core.RawDataBatcher.FeatureProxy

setTheId(int) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter.RawDataProxy

setTheId(int) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter.ReporterProxy

setTheId(int, String) - Method in class net.sf.basedb.core.RawDataBatcher.ReporterProxy

setThousandsSeparator(SessionControl, Character) - Static method in class net.sf.basedb.clients.web.formatter.FormatterSettings

Set the separator character to use as a "thousands" separator in large numbers.

setTime(int, Date) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setTime(String, Date) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setTime(Date) - Method in class net.sf.basedb.core.data.ChangeHistoryData

setTimeout(int) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper

setTimeout(int) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

setTimeout(int) - Method in class net.sf.basedb.util.uri.http.HttpConnectionManager

Set a timeout in seconds to allocate for the request to return (not including downloading of data).

setTimeSent(Date) - Method in class net.sf.basedb.core.data.MessageData

setTimestamp(int, Date) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setTimestamp(String, Date) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

Deprecated.

setTimestampFormat(Formatter<Date>) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil

Set a date formatter to use for formatting cells with timestamp-like values.

setTimestampValues(List<Date>) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink

setTimstampFormat(String) - Method in class net.sf.basedb.util.excel.AutoFormatter

Set the data format template to use for timestamp values.

Setting - Class in net.sf.basedb.core

This is the base class for all setting items.

Setting(SettingData) - Constructor for class net.sf.basedb.core.Setting

SETTING - Enum constant in enum class net.sf.basedb.core.Item

The item is an Setting.

SettingData - Class in net.sf.basedb.core.data

SettingData() - Constructor for class net.sf.basedb.core.data.SettingData

SettingInfo(String, boolean) - Constructor for class net.sf.basedb.core.SessionControl.SettingInfo

settings - Variable in class net.sf.basedb.clients.jobagent.JobRunner

settings - Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl

settings - Variable in class net.sf.basedb.clients.web.extensions.service.ServicesEventHandler

settings - Variable in class net.sf.basedb.core.data.ContextData

settings - Variable in class net.sf.basedb.core.ItemContext

settings - Variable in class net.sf.basedb.core.Presets.Preset

The key-value pairs in this preset.

settings - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsManager

settings - Variable in class net.sf.basedb.util.extensions.manager.filter.InstalledFilter

settings - Variable in class net.sf.basedb.util.extensions.manager.Settings

Settings - Class in net.sf.basedb.util.extensions.manager

Class for keeping settings for the extensions system.

Settings(ExtensionsManager, File) - Constructor for class net.sf.basedb.util.extensions.manager.Settings

Create a new Settings object.

setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean

setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

Set the title of the menu item in all cases.

setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean

setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean

setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory

setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean

setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory

setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory

setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean

setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean

setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory

setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

Set the title of the button in all cases.

setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.Button

setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.CalendarButton

The title attribute now goes into the calendar popup dialog instead.

setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.HideableSection

setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.Input

setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem

setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu

setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.Page

setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.path.PathElement

setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.tab.Tab

setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.table.Button

setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.table.Label

setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.table.Table

setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.Zoom

setTitle(String) - Method in class net.sf.basedb.core.data.ExperimentData

setTitle(String) - Method in class net.sf.basedb.core.data.ReporterClonePropertyData

setTitle(String) - Method in class net.sf.basedb.core.Experiment

Set the title for the publication of this experiment.

setTitle(String) - Method in class net.sf.basedb.util.export.spotdata.AnnotationAssayField

Set a custom title for the assay field.

setTitle(String) - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField

Set the title of the exported property.

setTitle(String) - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField

Set the column header title.

setTitle(String) - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField

Set the column header title.

setTo(BasicItem) - Method in class net.sf.basedb.core.AnyToAny

Set the destination item of the link.

setTo(UserData) - Method in class net.sf.basedb.core.data.MessageData

setTo(UserData) - Method in class net.sf.basedb.core.Message

Set the user this message should be sent to.

setToId(int) - Method in class net.sf.basedb.core.data.AnyToAnyData

setToken(String) - Method in class net.sf.basedb.core.data.UserDeviceData

setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo

setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean

setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

Set the tooltip of the menu item in all cases.

setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory

setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory

setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean

setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean

setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory

setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

Set the tooltip of the button in all cases.

setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.Button

setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.Help

setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.Icon

setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem

setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu

setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.path.PathElement

setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.PropertyValue

setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.tab.Tab

setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.table.Button

setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.table.Label

setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.Zoom

setTotalrows(int) - Method in class net.sf.basedb.clients.web.taglib.table.Navigator

setTotalrows(long) - Method in class net.sf.basedb.clients.web.taglib.table.Navigator

setTotalrows(String) - Method in class net.sf.basedb.clients.web.taglib.table.Navigator

setToType(int) - Method in class net.sf.basedb.core.data.AnyToAnyData

setTransferredBytes(long) - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress

Sets the number of transferred bytes.

setTransformation(TransformationData) - Method in class net.sf.basedb.core.data.BioAssaySetData

setTransformation(Transformation) - Method in class net.sf.basedb.core.BioAssaySet

Set the transformation that created this bioassayset.

setTransformation(Transformation) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter

Set the destination transformation.

setTransformation(Transformation) - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter

Set the destination transformation.

setTransformations(Set<TransformationData>) - Method in class net.sf.basedb.core.data.BioAssaySetData

setTransformations(Set<TransformationData>) - Method in class net.sf.basedb.core.data.ExperimentData

setTransformations(Set<TransformationData>) - Method in class net.sf.basedb.core.data.JobData

setTransformations(Set<TransformationData>) - Method in class net.sf.basedb.core.data.RawBioAssayData

setTray(String) - Method in class net.sf.basedb.core.BioPlate

Set the tray within the "storage location" for this bioplate.

setTray(String) - Method in class net.sf.basedb.core.data.BioPlateData

setTrimQuotes(boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser

Set if quotes around each data value should be removed or not.

setTrimWhiteSpace(boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser

Set a flag indicating if white-space should be trimmed from start and end of data values.

setTrusted(boolean) - Method in class net.sf.basedb.core.data.PluginDefinitionData

setTrusted(boolean) - Method in class net.sf.basedb.core.PluginDefinition

Set if this plugin should be trusted or not.

setTrusted(Boolean) - Method in class net.sf.basedb.core.data.JobAgentSettingsData

setTrusted(Boolean) - Method in class net.sf.basedb.core.JobAgentSettings

Set the trusted flag for this plugin.

setType(int) - Method in class net.sf.basedb.core.data.FormulaData

setType(int) - Method in class net.sf.basedb.core.data.JobData

setType(String) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

setType(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

Set the type of menu.

setType(String) - Method in class net.sf.basedb.clients.web.taglib.Input

setType(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Menu

setType(String) - Method in class net.sf.basedb.clients.web.taglib.Page

setType(String) - Method in class net.sf.basedb.plugins.executor.ParameterDefinition

Set the type of the parameter.

setType(MenuItemAction.MenuType) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

setType(MenuItemAction.MenuType) - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean

setType(MenuItemAction.MenuType) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

Set the type of the menu.

setType(Plugin.MainType) - Method in class net.sf.basedb.util.extensions.xml.PluginInfo

setType(Type) - Method in class net.sf.basedb.core.query.QueryParameter

Changes the type of the parameter.

setType(Type) - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField

Set the data type of the exported property.

setType(Type) - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField

Set the data type of the exported field.

setType(Type) - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField

Set the data type of the exported field.

setUninstalled() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile

Mark the file as uninstalled.

setUninstalledFile(File) - Method in class net.sf.basedb.util.extensions.manager.Settings

Mark the given file as uninstalled.

setUnit(UnitData) - Method in class net.sf.basedb.core.data.AnnotationData

setUnit(UnitData) - Method in class net.sf.basedb.core.data.PropertyFilterData

setUnit(UnitData) - Method in class net.sf.basedb.core.data.UnitSymbolData

setUnit(Unit) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

setUnit(Unit) - Method in class net.sf.basedb.core.PropertyFilter

Sets the unit the values for the property are stored in the database.

setUnits(Set<UnitData>) - Method in class net.sf.basedb.core.data.QuantityData

setUnselectedtext(String) - Method in class net.sf.basedb.clients.web.taglib.Select

setUpdateSource(String) - Method in class net.sf.basedb.core.ReporterBatcher

Set the source that was used when updating the reporters.

setUpErrorHandling() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

Initialise the error handling system.

setUpErrorHandling() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter

Don't use AbstractFlatFileImporter to handle errors.

setUpErrorHandling() - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Don't use AbstractFlatFileImporter to handle errors.

setUrl(String) - Method in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean

setUrl(String) - Method in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory

setUrl(String) - Method in class net.sf.basedb.clients.web.extensions.startpage.StartPageBean

setUrl(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem

setUrl(String) - Method in class net.sf.basedb.core.authentication.ExtraUserInformation

setUrl(String) - Method in class net.sf.basedb.core.data.FileData

setUrl(String) - Method in class net.sf.basedb.core.data.PluginDefinitionData

setUrl(String) - Method in class net.sf.basedb.core.data.UserData

setUrl(String) - Method in class net.sf.basedb.core.PluginDefinition

Set the URL to a web page with more information about the plug-in.

setUrl(String) - Method in class net.sf.basedb.core.User

Set the URL to the user's homepage, or null if unknown.

setUrl(String) - Method in class net.sf.basedb.util.extensions.AboutBean

setUrl(String, boolean) - Method in class net.sf.basedb.core.File

Set the URL to an external file that should represent this file object.

setUrl(String, UriMetadata) - Method in class net.sf.basedb.core.File

Set the URL to an external file that should represent this file object and update the metadata without going to the remote server.

setUsableUnits(Set<UnitData>) - Method in class net.sf.basedb.core.data.AnnotationTypeData

setUseClonedReporters(boolean) - Method in interface net.sf.basedb.core.ClonableReporterQuery

Set if cloned reporters should be used by default or not.

setUseClonedReporters(boolean) - Method in class net.sf.basedb.core.DynamicQuery

Set if cloned reporters should be used by default or not.

setUseClonedReporters(boolean) - Method in class net.sf.basedb.core.DynamicReporterQuery

Set if cloned reporters should be used by default or not.

setUseDeviceVerification(boolean) - Method in class net.sf.basedb.core.data.UserData

setUseDeviceVerification(boolean) - Method in class net.sf.basedb.core.User

Enable or disable device verification for this user account.

setUsedQuantity(Float) - Method in class net.sf.basedb.core.BioMaterialEvent

Set the used quantity.

setUsedQuantity(Float) - Method in class net.sf.basedb.core.BioMaterialEventSource

Set the quantity that was used from the source biomaterial by the event.

setUsedQuantity(Float) - Method in class net.sf.basedb.core.data.BioMaterialEventData

setUsedQuantity(Float) - Method in class net.sf.basedb.core.data.BioMaterialEventSourceData

setUsedUnits(Set<AnnotationTypeData>) - Method in class net.sf.basedb.core.data.UnitData

setUseInternalJobQueue(boolean) - Method in class net.sf.basedb.core.data.PluginDefinitionData

setUseInternalJobQueue(boolean) - Method in class net.sf.basedb.core.PluginDefinition

Set if the plug-in can use the internal job queue or not.

setUseNullIfEmpty(boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser

Specify if null values should be returned instead of empty strings for columns that doesn't contain any value.

setUseNullIfException(boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser

Specify if null should be returned if a (numeric) value can't be parsed.

setUseNullIfNull(boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser

Specify if null values should be returned for strings having the value "NULL" (ignoring case).

setUseNullLoaderIfNotFound(boolean) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory

Set a flag that determines if a NullNodeLoader should be used or if an ItemNotFoundException should be thrown if no registered node loader is found for a specific key.

setUsePermissions(boolean) - Method in class net.sf.basedb.core.data.PluginDefinitionData

setUsePermissions(boolean) - Method in class net.sf.basedb.core.PluginDefinition

setUser(UserData) - Method in class net.sf.basedb.core.data.BioMaterialEventData

setUser(UserData) - Method in class net.sf.basedb.core.data.ChangeHistoryData

setUser(UserData) - Method in class net.sf.basedb.core.data.ContextData

setUser(UserData) - Method in class net.sf.basedb.core.data.DiskUsageData

setUser(UserData) - Method in class net.sf.basedb.core.data.PasswordData

setUser(UserData) - Method in class net.sf.basedb.core.data.PlateEventData

setUser(UserData) - Method in class net.sf.basedb.core.data.SessionData

setUser(UserData) - Method in class net.sf.basedb.core.data.UserClientSettingData

setUser(UserData) - Method in class net.sf.basedb.core.data.UserDefaultSettingData

setUser(UserData) - Method in class net.sf.basedb.core.data.UserDeviceData

setUser(User) - Method in class net.sf.basedb.core.UserClientSetting

Set the user this setting is valid for.

setUser(User) - Method in class net.sf.basedb.core.UserDefaultSetting

Set the user this setting is valid for.

setUserAgent(String) - Method in class net.sf.basedb.core.data.UserDeviceData

setUserClientSetting(String, String) - Method in class net.sf.basedb.core.SessionControl

Set the value of a UserClientSetting.

setUserDefaultSetting(String, String) - Method in class net.sf.basedb.core.SessionControl

Set the value of a UserDefaultSetting.

setUserId(int) - Method in class net.sf.basedb.core.authentication.LoginRequest

Set the user id to use.

setUserId(int) - Method in class net.sf.basedb.core.data.ChangeHistoryData

setUserId(int) - Method in class net.sf.basedb.core.data.keyring.UserGroups

Set the id of the user.

setUserId(int) - Method in class net.sf.basedb.core.data.keyring.UserKeys

Set the id of the user.

setUserId(int) - Method in class net.sf.basedb.core.data.keyring.UserProjects

Set the id of the user.

setUserId(int) - Method in class net.sf.basedb.core.data.keyring.UserRoles

Set the id of the user.

setUsername(String) - Method in class net.sf.basedb.core.data.FileServerData

setUsername(String) - Method in class net.sf.basedb.core.FileServer

Set the username that is required to authenticate with the file server.

setUsername(String) - Method in class net.sf.basedb.util.uri.ConnectionParameters

setUsers(Map<UserData, Integer>) - Method in class net.sf.basedb.core.data.ItemKeyData

setUsers(Map<UserData, Integer>) - Method in class net.sf.basedb.core.data.ProjectData

setUsers(Set<UserData>) - Method in class net.sf.basedb.core.data.GroupData

setUsers(Set<UserData>) - Method in class net.sf.basedb.core.data.RoleData

setUserSettings(Set<UserClientSettingData>) - Method in class net.sf.basedb.core.data.ClientData

setUseSeparateConnections(boolean) - Method in class net.sf.basedb.core.hibernate.SessionFactoryConfiguration

Deprecated.

Set to TRUE to use connections separate from BASE connections.

setUseSeparateConnections(boolean) - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration

Set to TRUE to use connections separate from BASE connections.

setUsingColors(boolean) - Method in class net.sf.basedb.core.Coloring

Specifiy if colors should be used when displaying values for this item or not.

setUsingColors(boolean) - Method in class net.sf.basedb.core.data.ColoringData

setUsingTo(boolean) - Method in class net.sf.basedb.core.AnyToAny

If this link counts as using the destination item.

setUsingTo(boolean) - Method in class net.sf.basedb.core.data.AnyToAnyData

setUsNullValidatorIfNotFound(boolean) - Method in class net.sf.basedb.util.overview.validator.BasicItemNodeValidatorFactory

Set a flag that determines if a NullNodeValidator should be used or if an ItemNotFoundException should be thrown if no registered node validator is found for a specific key.

setValid(Boolean) - Method in class net.sf.basedb.core.data.FileSetMemberData

setValid(Boolean, String) - Method in class net.sf.basedb.core.FileSetMember

Set the validation status of this member.

setValue(int) - Method in class net.sf.basedb.clients.web.taglib.Input

setValue(Object) - Method in class net.sf.basedb.clients.web.taglib.table.Cell

setValue(Object) - Method in class net.sf.basedb.clients.web.taglib.table.CellValue

setValue(Object) - Method in class net.sf.basedb.core.query.QueryParameter

Change the value of the parameter.

setValue(String) - Method in class net.sf.basedb.clients.web.taglib.Input

setValue(String) - Method in class net.sf.basedb.clients.web.taglib.table.Hidden

setValue(String) - Method in class net.sf.basedb.core.data.PropertyFilterData

setValue(String) - Method in class net.sf.basedb.core.data.SettingData

setValue(String) - Method in class net.sf.basedb.core.PropertyFilter

Set the value to use in the filter.

setValue(String) - Method in class net.sf.basedb.core.Setting

Set the value for this setting.

setValue(String, ParameterType<T>, T) - Method in class net.sf.basedb.core.ParameterValuesImpl

setValue(String, ParameterType<T>, T) - Method in class net.sf.basedb.core.plugin.NamespaceParameterValuesWrapper

setValue(String, ParameterType<T>, T) - Method in interface net.sf.basedb.core.plugin.ParameterValues

Set a single value for a parameter.

setValue(String, ParameterType<T>, T) - Method in class net.sf.basedb.core.plugin.ParameterValuesWrapper

Set the value on either the job or configuration, depending in the preferJob parameter that was set when creating this object.

setValue(String, ParameterType<T>, T) - Method in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues

setValue(AnnotationType, Object, Unit, boolean) - Method in class net.sf.basedb.core.AnnotationBatcher

Add, update or delete a single-valued annotation.

setValueId(int) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink

setValueIfDifferent(Object, Unit) - Method in class net.sf.basedb.core.Annotation

Set the value of the annotation, replacing any previous values if they are different.

setValues(String, ParameterType<T>, List<T>) - Method in class net.sf.basedb.core.ParameterValuesImpl

setValues(String, ParameterType<T>, List<T>) - Method in class net.sf.basedb.core.plugin.NamespaceParameterValuesWrapper

setValues(String, ParameterType<T>, List<T>) - Method in interface net.sf.basedb.core.plugin.ParameterValues

Set a list of values for a parameter.

setValues(String, ParameterType<T>, List<T>) - Method in class net.sf.basedb.core.plugin.ParameterValuesWrapper

Set the value on either the job or configuration, depending in the preferJob parameter that was set when creating this object.

setValues(String, ParameterType<T>, List<T>) - Method in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues

setValues(List<?>) - Method in class net.sf.basedb.core.AnnotationType

Set the list of allowed values for an enumerated annotation type.

setValues(List<?>) - Method in class net.sf.basedb.plugins.executor.ProgramParameter

setValues(List<Boolean>) - Method in class net.sf.basedb.core.data.BooleanParameterValueData

setValues(List<Double>) - Method in class net.sf.basedb.core.data.DoubleParameterValueData

setValues(List<Float>) - Method in class net.sf.basedb.core.data.FloatParameterValueData

setValues(List<Integer>) - Method in class net.sf.basedb.core.data.IntegerParameterValueData

setValues(List<Long>) - Method in class net.sf.basedb.core.data.LongParameterValueData

setValues(List<String>) - Method in class net.sf.basedb.core.data.StringParameterValueData

setValues(List<String>) - Method in class net.sf.basedb.core.data.TextParameterValueData

setValues(List<Date>) - Method in class net.sf.basedb.core.data.DateParameterValueData

setValues(List<Date>) - Method in class net.sf.basedb.core.data.TimestampParameterValueData

setValues(List<BasicData>) - Method in class net.sf.basedb.core.data.ItemParameterValueData

setValues(List<T>) - Method in class net.sf.basedb.core.data.ParameterValueData

Set values of this parameter.

setValues(AnnotationType, List<?>, Unit, boolean) - Method in class net.sf.basedb.core.AnnotationBatcher

Add, update or delete annotation values for the current item.

setValues(ParameterValueData<?>) - Method in class net.sf.basedb.core.data.AnnotationData

setValuesIfDifferent(List<?>, Unit) - Method in class net.sf.basedb.core.Annotation

Set the values of the annotation, replacing any previous values if they are different.

setValueType(int) - Method in class net.sf.basedb.core.data.AnnotationTypeData

setValueType(int) - Method in class net.sf.basedb.core.data.DataCubeExtraValueData

setValueType(int) - Method in class net.sf.basedb.core.data.ExtraValueTypeData

setValueType(int) - Method in class net.sf.basedb.core.data.PropertyFilterData

setValueType(int) - Method in class net.sf.basedb.core.data.ReporterClonePropertyData

setValueType(Integer) - Method in class net.sf.basedb.core.data.FormulaData

setValueType(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

setValueType(Type) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

setValueType(Type) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef

setValueType(Type) - Method in class net.sf.basedb.core.DataCubeExtraValue

Set the value type.

setValueType(Type) - Method in class net.sf.basedb.core.ExtraValueType

Set the value type for this extra value type.

setValueType(Type) - Method in class net.sf.basedb.core.Formula

Set the type of the values that this formula produces.

setValueType(Type) - Method in class net.sf.basedb.core.PropertyFilter

Set the type of the property.

setVariable(String, String) - Method in class net.sf.basedb.util.extensions.xml.VariableConverter

Set the value of a variable.

setVariant(PlatformVariantData) - Method in class net.sf.basedb.core.data.ArrayDesignData

setVariant(PlatformVariantData) - Method in class net.sf.basedb.core.data.FileTypeIndex

setVariant(PlatformVariantData) - Method in class net.sf.basedb.core.data.PlatformFileTypeData

setVariant(PlatformVariantData) - Method in class net.sf.basedb.core.data.RawBioAssayData

setVariant(PlatformVariant) - Method in class net.sf.basedb.core.ArrayDesign

Set the platform and variant of the array design.

setVariant(PlatformVariant, RawDataType) - Method in class net.sf.basedb.core.RawBioAssay

Set the platform and variant of the raw bioassay.

setVariants(Set<PlatformVariantData>) - Method in class net.sf.basedb.core.data.PlatformData

setVerified(boolean) - Method in class net.sf.basedb.core.data.UserDeviceData

setVerifyOnly(boolean) - Method in class net.sf.basedb.core.authentication.LoginRequest

Set a flag to indicate if the login request should only verify the login parameters and not do a full login.

setVersion(int) - Method in class net.sf.basedb.core.data.BasicData

Set the version of the item.

setVersion(int) - Method in class net.sf.basedb.core.data.VersionedParameter

setVersion(String) - Method in class net.sf.basedb.util.extensions.AboutBean

setVersionString(String) - Method in class net.sf.basedb.core.data.HardwareData

setVersionString(String) - Method in class net.sf.basedb.core.data.PluginDefinitionData

setVersionString(String) - Method in class net.sf.basedb.core.data.SoftwareData

setVersionString(String) - Method in class net.sf.basedb.core.Hardware

Set the versionstring for this Hardware item.

setVersionString(String) - Method in class net.sf.basedb.core.PluginDefinition

Update version information for this plug-in.

setVersionString(String) - Method in class net.sf.basedb.core.Software

Set the versionstring for this Software item.

setVertical(boolean) - Method in class net.sf.basedb.clients.web.taglib.ButtonGroup

setVirtualDb(VirtualDbData) - Method in class net.sf.basedb.core.data.DataCubeData

setVirtualDb(VirtualDbData) - Method in class net.sf.basedb.core.data.ExperimentData

setVirtualDb(VirtualDb) - Method in class net.sf.basedb.core.DataCube

Set the experiment.

setVisible(boolean) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

setVisible(boolean) - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean

setVisible(boolean) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory

setVisible(boolean) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory

setVisible(boolean) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean

setVisible(boolean) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean

setVisible(boolean) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory

setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.Button

setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.Help

setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.HideableSection

setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.Icon

setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.Input

setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem

setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.menu.Menuseparator

setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu

setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.path.PathElement

setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.Select

setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.tab.Tab

setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Button

setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Cell

setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Header

setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Label

setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Navigator

setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Panel

setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector

setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Row

setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Toolbar

setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.Zoom

setVisible(String) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

setVisible(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory

setVisible(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory

setVisible(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory

setVisiblePermission(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

Set the minimum permission that is required to make the menu item visible.

setVisiblePermission(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

Set the minimum permission that is required to make the button visible.

setWarnings(int) - Method in class net.sf.basedb.util.overview.Node

Set the number of warnings that was found while validating this node.

setWell(WellData) - Method in class net.sf.basedb.core.data.FeatureData

setWells(Map<PlateCoordinate, WellData>) - Method in class net.sf.basedb.core.data.PlateData

setWidth(int) - Method in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean

setWidth(int) - Method in class net.sf.basedb.clients.web.taglib.table.Form

setWidth(int) - Method in class net.sf.basedb.core.AnnotationType

Set the recommended width in characters a client application should use to render an input field for annotations of this annotation type.

setWidth(int) - Method in class net.sf.basedb.core.data.AnnotationTypeData

setWidth(String) - Method in class net.sf.basedb.clients.web.extensions.plot.MAPlotFactory

setWorkerThread() - Method in class net.sf.basedb.core.signal.EnhancedThreadSignalHandler

Set the worker thread to the current thread.

setWorkerThread(Thread) - Method in class net.sf.basedb.core.signal.ThreadSignalHandler

Set the worker thread that should be interrupted when a signal is receiver.

setWrapper(WrappingRenderer<?>) - Method in class net.sf.basedb.clients.web.taglib.extensions.Render

setWriteProtected(boolean) - Method in class net.sf.basedb.core.data.FileData

setWriteProtected(boolean) - Method in class net.sf.basedb.core.File

Set the write protected flag for this file.

setWriter(BaseFileWriter) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter

Set the stream were the exported data should be written.

setWriteTrailingColumns(boolean) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil

setX(Float) - Method in class net.sf.basedb.core.data.RawData

setY(Float) - Method in class net.sf.basedb.core.data.RawData

severities - Variable in class net.sf.basedb.util.overview.ValidationOptions

Maps Validator ID to severity.

Severity - Enum Class in net.sf.basedb.util.overview

Severity levels for a validation rule.

Severity(String) - Constructor for enum class net.sf.basedb.util.overview.Severity

sf - Static variable in class net.sf.basedb.core.HibernateUtil

The single SessionFactory.

SHA256_FINGERPRINT_PATTERN - Static variable in class net.sf.basedb.core.FileServer

Pattern that matches a SSH SHa256 fingerprint in BASE64 encoding (padding is optional).

SHARE_TO_EVERYONE - Enum constant in enum class net.sf.basedb.core.Permission

This permission allows a user to share an item to the Group.EVERYONE group.

shareable - Static variable in class net.sf.basedb.core.Item.DefinedPermissions

Shareable - Interface in net.sf.basedb.core

An Shareable item is an item which can be shared to other User:s, Group:s and Project:s.

shareable_annotatable - Static variable in class net.sf.basedb.core.Item.DefinedPermissions

SHAREABLE_FILTER - Static variable in class net.sf.basedb.core.QueryRuntimeFilterFactory

ShareableData - Interface in net.sf.basedb.core.data

A shareable item is an item which can be shared to other users, groups or projects.

ShareableFilter() - Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.ShareableFilter

shareableItems - Static variable in class net.sf.basedb.core.Metadata

ShareableUtil - Class in net.sf.basedb.core

Utility methods that will make it easier to implement the Shareable interface, including data validation.

ShareableUtil - Class in net.sf.basedb.util

ShareableUtil() - Constructor for class net.sf.basedb.core.ShareableUtil

ShareableUtil() - Constructor for class net.sf.basedb.util.ShareableUtil

SHARED - Enum constant in enum class net.sf.basedb.core.Include

Include items shared to the logged in user.

SharedData - Class in net.sf.basedb.core.data

This class extends the OwnedData class and implements the ShareableData interface.

SharedData() - Constructor for class net.sf.basedb.core.data.SharedData

SharedItem - Class in net.sf.basedb.core

This class inherits from the OwnedItem class and implements the Shareable interface.

SharedItem(SharedData) - Constructor for class net.sf.basedb.core.SharedItem

sharedTo - Variable in class net.sf.basedb.core.query.SharedToRestriction

sharedTo(boolean, Restriction, Restriction, Restriction) - Static method in class net.sf.basedb.core.query.Hql

A special restriction that works on Shareable items.

SharedToRestriction - Class in net.sf.basedb.core.query

A special restriction that works on Shareable items.

SharedToRestriction(boolean, Restriction, Restriction, Restriction) - Constructor for class net.sf.basedb.core.query.SharedToRestriction

shareRecursively(DbControl, Directory) - Static method in class net.sf.basedb.core.ShareableUtil

Share all files and sub-directories in the given directory with the same permissions.

sheet - Variable in class net.sf.basedb.clients.web.plugins.XlsxTemplate

sheet - Variable in class net.sf.basedb.util.excel.XlsxTableWriter

sheet - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo

sheet - Variable in class net.sf.basedb.util.parser.FlatFileParser.ExcelData

SheetInfo(Sheet) - Constructor for class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo

sheetNames - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil

sheets - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil

SHORT - Enum constant in enum class net.sf.basedb.core.Job.ExecutionTime

The job shouldn't take more than 10 minutes to execute.

SHORT - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper

SHORTEST - Enum constant in enum class net.sf.basedb.core.Job.ExecutionTime

The job is fast and should not take more than a minute to execute.

shortName - Variable in class net.sf.basedb.core.data.AnnotationTypeCategoryData

ShortWriter - Class in net.sf.basedb.core.migrate

Database-independent writer implementation that writes short values from a result set.

ShortWriter(ResultSet, int, Writer, char[]) - Constructor for class net.sf.basedb.core.migrate.ShortWriter

shouldManageNamespaces() - Method in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget

shouldSend(EventType, ExtensionPoint<?>, Extension<?>) - Method in class net.sf.basedb.util.extensions.events.ActionClassEventFilter

shouldSend(EventType, ExtensionPoint<?>, Extension<?>) - Method in class net.sf.basedb.util.extensions.events.AllEventsFilter

shouldSend(EventType, ExtensionPoint<?>, Extension<?>) - Method in class net.sf.basedb.util.extensions.events.CombiningEventFilter

shouldSend(EventType, ExtensionPoint<?>, Extension<?>) - Method in interface net.sf.basedb.util.extensions.events.EventFilter

Determine if the event should be sent to the event handler or not.

shouldSend(EventType, ExtensionPoint<?>, Extension<?>) - Method in class net.sf.basedb.util.extensions.events.EventTypeFilter

shouldSend(EventType, ExtensionPoint<?>, Extension<?>) - Method in class net.sf.basedb.util.extensions.events.ExtensionEventFilter

shouldSend(EventType, ExtensionPoint<?>, Extension<?>) - Method in class net.sf.basedb.util.extensions.events.ExtensionPointEventFilter

show - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef

If the column should be visible or not.

show - Variable in class net.sf.basedb.clients.web.taglib.table.TableColumn

showChangeHistoryTab(SessionControl) - Static method in class net.sf.basedb.clients.web.ChangeHistoryUtil

Check if the "Change history" tab should be visible for the current user or not.

showClass - Variable in class net.sf.basedb.clients.web.taglib.HideableSection

showClazz - Variable in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory

showClazz - Variable in class net.sf.basedb.clients.web.extensions.section.SectionBean

showInitially - Variable in class net.sf.basedb.clients.web.taglib.HideableSection

If the section should be shown or hidden to start with.

shutdown(CloseableHttpClient) - Static method in class net.sf.basedb.util.HttpUtil

Safely shuts down a http client and it's connection manager without trowing an exception.

SHUTDOWN - Static variable in class net.sf.basedb.core.signal.Signal

The SHUTDOWN signal, that requests that the receiver should clean up and die.

ShutdownHook(SignalReceiver) - Constructor for class net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor.ShutdownHook

ShutdownSignalSender - Class in net.sf.basedb.core.signal

A signal sender implementation that is used by the system when shutting down.

ShutdownSignalSender() - Constructor for class net.sf.basedb.core.signal.ShutdownSignalSender

signal - Variable in class net.sf.basedb.core.signal.ExtensionSignalTransporter.SendSignalRenderer

signal - Variable in class net.sf.basedb.core.signal.SimpleSignalSender

signal - Variable in exception net.sf.basedb.core.signal.UnsupportedSignalException

Signal - Class in net.sf.basedb.core.signal

Represents a signal that can be sent to a class implementing the SignalTarget interface.

Signal(String, String, String) - Constructor for class net.sf.basedb.core.signal.Signal

SignalException - Exception in net.sf.basedb.core.signal

Base class for all signal exceptions.

SignalException() - Constructor for exception net.sf.basedb.core.signal.SignalException

SignalException(String) - Constructor for exception net.sf.basedb.core.signal.SignalException

SignalException(String, Throwable) - Constructor for exception net.sf.basedb.core.signal.SignalException

SignalException(Throwable) - Constructor for exception net.sf.basedb.core.signal.SignalException

signalHandler - Variable in class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor

signalHandler - Variable in class net.sf.basedb.clients.web.plugins.SimpleExport

signalHandler - Variable in class net.sf.basedb.plugins.AbstractFlatFileImporter

signalHandler - Variable in class net.sf.basedb.plugins.Base1PluginExecuter

signalHandler - Variable in class net.sf.basedb.plugins.BaseFileExporterPlugin

signalHandler - Variable in class net.sf.basedb.plugins.BfsExporterPlugin

signalHandler - Variable in class net.sf.basedb.plugins.CdfFileReporterImporter

signalHandler - Variable in class net.sf.basedb.plugins.CloneReportersPlugin

signalHandler - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

signalHandler - Variable in class net.sf.basedb.plugins.FormulaFilter

signalHandler - Variable in class net.sf.basedb.plugins.GalExporter

signalHandler - Variable in class net.sf.basedb.plugins.HelpExporter

signalHandler - Variable in class net.sf.basedb.plugins.HelpImporter

signalHandler - Variable in class net.sf.basedb.plugins.IntensityCalculatorPlugin

signalHandler - Variable in class net.sf.basedb.plugins.JepExtraValueCalculator

signalHandler - Variable in class net.sf.basedb.plugins.JepIntensityTransformer

signalHandler - Variable in class net.sf.basedb.plugins.LowessNormalization

signalHandler - Variable in class net.sf.basedb.plugins.MedianRatioNormalization

signalHandler - Variable in class net.sf.basedb.plugins.PackedFileExporter

signalHandler - Variable in class net.sf.basedb.plugins.PlateMappingExporter

signalHandler - Variable in class net.sf.basedb.plugins.PluginConfigurationExporter

signalHandler - Variable in class net.sf.basedb.plugins.PluginConfigurationImporter

signalHandler - Variable in class net.sf.basedb.util.zip.AbstractFileUnpacker

SignalHandler - Interface in net.sf.basedb.core.signal

A signal handler is an object that is able to receive and act on signals.

signalHandlerURI - Variable in class net.sf.basedb.core.signal.AbstractSignalTransporter

SignalKeyring() - Constructor for class net.sf.basedb.core.Job.SignalKeyring

SignalReceivedException - Exception in net.sf.basedb.core.signal

This exception can be thrown by signal handlers when one or more signal has been received.

SignalReceivedException(List<Signal>) - Constructor for exception net.sf.basedb.core.signal.SignalReceivedException

Create a new SignalReceivedException when multiple signals has been received.

SignalReceivedException(Signal) - Constructor for exception net.sf.basedb.core.signal.SignalReceivedException

Create a new UnsupportedSignalException.

SignalReceivedException(Signal...) - Constructor for exception net.sf.basedb.core.signal.SignalReceivedException

Create a new SignalReceivedException when multiple signals has been received.

signalReceiver - Variable in class net.sf.basedb.clients.jobagent.Agent

signalReceiver - Variable in class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor

signalReceiver - Variable in class net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor.ShutdownHook

signalReceiver - Variable in class net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor

signalReceiver - Variable in class net.sf.basedb.clients.jobagent.handlers.SignalRequestHandler

signalReceiver - Static variable in class net.sf.basedb.core.InternalJobQueue

Use the local signal receiver only.

signalReceiver - Variable in class net.sf.basedb.core.PluginExecutionRequest

SignalReceiver - Interface in net.sf.basedb.core.signal

A signal receiver is a class that knows how to receive a Signal from a SignalTransporter and how to distribute this to a SignalHandler.

SignalRequestHandler - Class in net.sf.basedb.clients.jobagent.handlers

This is a request handler for the signal commands.

SignalRequestHandler(Agent) - Constructor for class net.sf.basedb.clients.jobagent.handlers.SignalRequestHandler

signals - Variable in class net.sf.basedb.core.signal.AbstractSignalTransporter

signals - Static variable in class net.sf.basedb.core.signal.Signal

Holds all registered signals.

signals - Variable in exception net.sf.basedb.core.signal.SignalReceivedException

SignalSender - Interface in net.sf.basedb.core.signal

A signal sender is responsible for sending a signal to a signal handler.

SignalTarget - Interface in net.sf.basedb.core.signal

This interface should be implemented by classes that are able to receive Signal:s.

signalTransporter - Variable in class net.sf.basedb.core.data.JobData

signalTransporter - Variable in class net.sf.basedb.core.Job

SignalTransporter - Interface in net.sf.basedb.core.signal

A signal transporter is a class that knows how to send a signal to a specific SignalReceiver implementation.

silent - Variable in class net.sf.basedb.core.hibernate.DbIndexWork

simple(Expression, String, Type, Formula.AverageMethod, Formatter<?>) - Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory

Create a simple dynamic field.

SimpleAbsoluteProgressReporter - Class in net.sf.basedb.core

This is a simple implementation of the AbsoluteProgressReporter interface, which simply remembers that last values.

SimpleAbsoluteProgressReporter(ProgressReporter, long) - Constructor for class net.sf.basedb.core.SimpleAbsoluteProgressReporter

Create a new absolute progress reporter.

SimpleDynamicField - Class in net.sf.basedb.util.export.spotdata

Represents an exported data field.

SimpleDynamicField() - Constructor for class net.sf.basedb.util.export.spotdata.SimpleDynamicField

Create a new object.

SimpleErrorHandler - Class in net.sf.basedb.util.error

A simple error handler that either ignores all errors or re-throws them.

SimpleErrorHandler(boolean) - Constructor for class net.sf.basedb.util.error.SimpleErrorHandler

Create a new simple error handler.

SimpleExport - Class in net.sf.basedb.clients.web.plugins

Export plugin for exporting data from table listings in the web client.

SimpleExport() - Constructor for class net.sf.basedb.clients.web.plugins.SimpleExport

SimpleJepFunction - Class in net.sf.basedb.util.jep

A simple base class for registering a JEP function by name and number of parameters.

SimpleJepFunction(String, int) - Constructor for class net.sf.basedb.util.jep.SimpleJepFunction

SimpleProgressReporter - Class in net.sf.basedb.core

This is a simple implementation of the ProgressReporter interface, which simply remembers that last values.

SimpleProgressReporter(ProgressReporter) - Constructor for class net.sf.basedb.core.SimpleProgressReporter

Create a new simple progress reporter.

SimpleSignalProgressReporter - Class in net.sf.basedb.clients.web.util

This class can be used to report progress and hold signal receiver for those export plugins that download immediately.

SimpleSignalProgressReporter(ProgressReporter) - Constructor for class net.sf.basedb.clients.web.util.SimpleSignalProgressReporter

SimpleSignalSender - Class in net.sf.basedb.core.signal

A signal sender implementation that sends a specific signal to all handlers that supports it.

SimpleSignalSender(Signal) - Constructor for class net.sf.basedb.core.signal.SimpleSignalSender

Create a new signal sender.

SimpleStringDetector - Class in net.sf.basedb.util.charset

A simple string detector implementation that works with two strings.

SimpleStringDetector(String, String) - Constructor for class net.sf.basedb.util.charset.SimpleStringDetector

SINGLE_QUOTE - Static variable in class net.sf.basedb.clients.web.util.HTML

SingleExtensionFilter - Class in net.sf.basedb.util.extensions

A filter implementation that enables a single extension and disables all other.

SingleExtensionFilter(String) - Constructor for class net.sf.basedb.util.extensions.SingleExtensionFilter

Create a filter that enables the extension with the given ID and disables all others.

SingleExtensionFilter(Extension<?>) - Constructor for class net.sf.basedb.util.extensions.SingleExtensionFilter

Create a filter that enables the given extension and disables all other.

SingleFileValidationAction - Class in net.sf.basedb.util.fileset

Base class for validators that works on single files of a known data file type.

SingleFileValidationAction(String) - Constructor for class net.sf.basedb.util.fileset.SingleFileValidationAction

Create a new instance.

size - Variable in class net.sf.basedb.core.data.FileData

size - Variable in class net.sf.basedb.core.data.ItemListData

size - Variable in class net.sf.basedb.core.data.PhysicalBioAssayData

size - Variable in class net.sf.basedb.core.data.ReporterListData

size - Variable in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo

size - Variable in class net.sf.basedb.core.hibernate.TypeWrapper

size - Variable in class net.sf.basedb.core.log.EntityLogOptions

size - Variable in class net.sf.basedb.core.MigrateRbaToDba.Itemlist

size - Variable in class net.sf.basedb.core.VirtualColumn

The size of the column if it is a string.

size - Variable in class net.sf.basedb.util.JarClassLoader.JarInfo

size() - Method in class net.sf.basedb.clients.web.extensions.skin.ImageRemapper

Get the number of remapped images.

size() - Method in class net.sf.basedb.core.AnyToAny.FastLinkLoader

Number of items that matches.

size() - Method in class net.sf.basedb.core.GroupPermissions

Get the number of entries.

size() - Method in class net.sf.basedb.core.ItemResultList

size() - Method in class net.sf.basedb.core.Presets.Preset

Get the number of settings in the preset.

size() - Method in class net.sf.basedb.core.ProjectPermissions

Get the number of entries.

size() - Method in class net.sf.basedb.core.UserPermissions

Get the number of entries.

size() - Method in class net.sf.basedb.util.Enumeration

size() - Method in class net.sf.basedb.util.formatter.LookupFormatter

Get the number of registered lookup entries.

size() - Method in class net.sf.basedb.util.Tree

size(String) - Method in class net.sf.basedb.util.StaticCache

Checks the size (in bytes) of a cache entry.

size(String, String) - Static method in class net.sf.basedb.core.query.Hql

Create a size expression for a property that is a collection of values.

sizeAtLastSync - Variable in class net.sf.basedb.core.data.ItemListData

sizeColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter

sizeMapper - Variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter

sizeOf(Object) - Method in enum class net.sf.basedb.core.Type

Get the size in bytes an object of this type requires when stored in the database.

SkinAction - Interface in net.sf.basedb.clients.web.extensions.skin

Action for adding skins to BASE.

skinActions - Variable in class net.sf.basedb.clients.web.taglib.Page

skinContext - Variable in class net.sf.basedb.clients.web.taglib.Page

skip - Variable in class net.sf.basedb.clients.web.taglib.table.Hidden

If the hidden element should be included or not.

skip(long) - Method in class net.sf.basedb.util.InputStreamCombiner

skip(long) - Method in class net.sf.basedb.util.InputStreamSplitter

skip(long) - Method in class net.sf.basedb.util.InputStreamTracker

skipInsertIfMissingFeature - Variable in class net.sf.basedb.core.RawDataBatcher

If inserts that can't find a matching feature should be skipped or generate an error.

skipInsertIfMissingFeature(boolean) - Method in class net.sf.basedb.core.RawDataBatcher

Specify if the insert method should skip the insert if a feature for the spot can't be found.

skipNull - Variable in class net.sf.basedb.util.formatter.CollectionFormatter

skippedLast - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

skippedLines - Variable in class net.sf.basedb.plugins.AbstractFlatFileImporter

skippedLines - Variable in class net.sf.basedb.util.parser.FlatFileParser

List for keeping ignored and unknown lines in the FlatFileParser.nextData() method.

skipRepeatedTranscriptIds - Variable in class net.sf.basedb.util.gtf.GtfInputStream

SLIDES - Enum constant in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section

slot - Variable in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlot

slot - Variable in class net.sf.basedb.core.InternalJobQueue.JobRunner

slot - Variable in class net.sf.basedb.util.jobagent.JobInfo

Slot - Class in net.sf.basedb.clients.jobagent.slotmanager

Represents a slot that has been assigned to a job.

Slot(String, Job.ExecutionTime) - Constructor for class net.sf.basedb.clients.jobagent.slotmanager.Slot

Create a new slot.

Slot(Job.ExecutionTime) - Constructor for class net.sf.basedb.clients.jobagent.slotmanager.Slot

Create a new slot and automatically assign an id to it.

slotManager - Variable in class net.sf.basedb.clients.jobagent.Agent

SlotManager - Interface in net.sf.basedb.clients.jobagent.slotmanager

A slot manager is responsible for slot assigment to jobs.

slotManagerClass - Variable in class net.sf.basedb.clients.jobagent.Agent

SMART_IMAGES - Static variable in class net.sf.basedb.clients.web.util.HTML

This flag is used in HTML.scanForLinks(String,int) when you want to create links for images with a <img> tag instead of an <a> tag.

smartEnum - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef

snapshotIsInvalid - Variable in class net.sf.basedb.core.AnnotationSet

Flag to indicate if this annotation set has been modified and the snapshot must be removed.

snapshotManager - Variable in class net.sf.basedb.clients.web.ExperimentExplorer

The snapshot manager that loads annotation values.

snapshotManager - Variable in class net.sf.basedb.clients.web.plugins.BioAssayExperimentalFactorLoader

snapshotManager - Variable in class net.sf.basedb.util.annotations.InheritAnnotationsManager

snapshotManager - Variable in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

snapshotManager - Variable in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter

snapshotManager - Variable in class net.sf.basedb.util.export.spotdata.AnnotationAssayField

snapshotManager - Variable in class net.sf.basedb.util.overview.GenericOverview

SnapshotManager - Class in net.sf.basedb.core.snapshot

Manager for annotation snapshots.

SnapshotManager() - Constructor for class net.sf.basedb.core.snapshot.SnapshotManager

Create a new snapshot manager.

snapshots - Variable in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil

snapshots - Variable in class net.sf.basedb.core.snapshot.SnapshotManager

snapshotsToDelete - Variable in class net.sf.basedb.core.AnnotationBatcher

socket - Variable in class net.sf.basedb.core.signal.SocketSignalReceiver.ListenerThread

socket - Variable in class net.sf.basedb.util.jobagent.JobAgentServerConnection.ListenerThread

SocketSignalReceiver - Class in net.sf.basedb.core.signal

A signal receiver implementation that listens on a socket for incoming signals.

SocketSignalReceiver() - Constructor for class net.sf.basedb.core.signal.SocketSignalReceiver

Create a new socket signal receiver.

SocketSignalReceiver.ListenerThread - Class in net.sf.basedb.core.signal

This class is used for listening to the specified socket for incoming connections.

SocketSignalTransporter - Class in net.sf.basedb.core.signal

SocketSignalTransporter() - Constructor for class net.sf.basedb.core.signal.SocketSignalTransporter

Create a new socket signal transporter.

SocketUtil - Class in net.sf.basedb.util

This class contains some useful methods when working with sockets.

SocketUtil() - Constructor for class net.sf.basedb.util.SocketUtil

software - Variable in class net.sf.basedb.core.data.DerivedBioAssayData

software - Variable in class net.sf.basedb.core.data.RawBioAssayData

software - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter

Software - Class in net.sf.basedb.core

This class is used to represent individual software items and information about them.

Software(SoftwareData) - Constructor for class net.sf.basedb.core.Software

Creates a new software item.

SOFTWARE - Enum constant in enum class net.sf.basedb.core.Item

The item is a Software.

softwareColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

softwareColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

SoftwareData - Class in net.sf.basedb.core.data

This class holds information about a software.

SoftwareData() - Constructor for class net.sf.basedb.core.data.SoftwareData

softwareHasBeenSet - Variable in class net.sf.basedb.core.DerivedBioAssay

softwareHasBeenSet - Variable in class net.sf.basedb.core.RawBioAssay

softwareId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba

SoftwareLoader - Class in net.sf.basedb.util.overview.loader

Node loader implementation for software.

SoftwareLoader() - Constructor for class net.sf.basedb.util.overview.loader.SoftwareLoader

softwareMapper - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

softwareMapper - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

softwareQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

SoftwareValidator - Class in net.sf.basedb.util.overview.validator

Validator implementation for software.

SoftwareValidator() - Constructor for class net.sf.basedb.util.overview.validator.SoftwareValidator

sort(List<? extends InvokationContext<?>>) - Method in class net.sf.basedb.util.extensions.DefaultFilter

sort(List<? extends InvokationContext<?>>) - Method in interface net.sf.basedb.util.extensions.ExtensionsFilter

Sort a list of invoked extensions according to some property.

sort(List<? extends InvokationContext<?>>) - Method in class net.sf.basedb.util.extensions.SingleExtensionFilter

Do nothing since the list should contain only a single extension.

sortable - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

sortable - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

sortable - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef

If the column is sortable or not

sortable - Variable in class net.sf.basedb.clients.web.taglib.table.TableColumn

sortby - Variable in class net.sf.basedb.clients.web.taglib.table.Table

The column to sort by.

sortBy(Expression) - Method in enum class net.sf.basedb.core.ItemContext.SortDirection

Create an order expression that can be used with queries: Query.order(Order).

sortByAnnotationType(DbControl) - Static method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

Create a comparator for sorting annotation snapshots by the name of the annotation type.

sortByProject(DbControl, boolean) - Static method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

Create a comparator for sorting annotation snapshots by the name of the project.

SortByProjectComparator() - Constructor for class net.sf.basedb.core.snapshot.AnnotationSetSnapshot.SortByProjectComparator

sortChildren(Comparator<? super Node>) - Method in class net.sf.basedb.util.overview.Node

Sorts the list of child nodes.

sortColumns - Variable in class net.sf.basedb.clients.web.taglib.table.Table

sortDirection - Variable in class net.sf.basedb.clients.web.taglib.table.Table

ASC or DESC

sortDirection - Variable in class net.sf.basedb.core.data.ContextData

sortDirection - Variable in class net.sf.basedb.core.ItemContext

SortDirection(int, String) - Constructor for enum class net.sf.basedb.core.ItemContext.SortDirection

Creates a new direction.

sortKeys() - Method in class net.sf.basedb.util.Enumeration

This method will sort the enumration on the keys using Collections.sort(List, Comparator).

sortProperty - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

sortProperty - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

sortProperty - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef

Optional property used for sorting.

sortProperty - Variable in class net.sf.basedb.core.data.ContextData

sortProperty - Variable in class net.sf.basedb.core.ItemContext

sortValues() - Method in class net.sf.basedb.util.Enumeration

This method will sort the enumration on the values using Collections.sort(List, Comparator).

source - Variable in class net.sf.basedb.clients.web.extensions.DynamicActionAttributeSupport

source - Variable in class net.sf.basedb.core.data.AnnotationData

source - Variable in class net.sf.basedb.core.data.annotations.AnnotationLink

source - Variable in class net.sf.basedb.core.data.TransformationData

source - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot

source - Variable in class net.sf.basedb.util.annotations.InheritAnnotationsManager.AnnotationTypeFilter

source - Variable in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

source - Variable in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter

source - Variable in class net.sf.basedb.util.listable.AbstractSourceItemTransformer

source - Variable in class net.sf.basedb.util.listable.SourceItemTransformerChain

Source() - Constructor for enum class net.sf.basedb.core.Annotation.Source

SOURCE - Enum constant in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section

SOURCE_BIOASSAYS - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

SOURCE_BIOASSAYSET - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

SOURCE_DERIVEDBIOASSAY - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

sourceBioAssaySetParameter - Variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

The source parameter for bioassay set.

sourceBioAssaySetType - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

The parameter type for the source bioassay set.

sourceColumnMapper - Variable in class net.sf.basedb.plugins.PlateMappingImporter

sourceCount - Variable in class net.sf.basedb.core.data.PlateMappingData

sourceDerivedBioAssayParameter - Variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

The source parameter for derived bioassay.

sourceDerivedBioAssayType - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

The parameter type for the source derived bioassay.

sourceFile - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileImporter

sourceGeometry - Variable in class net.sf.basedb.core.data.PlateMappingData

sourceIdHash - Variable in class net.sf.basedb.util.listable.TransformCache.CacheKey

sourceIntensityTransform - Variable in class net.sf.basedb.core.data.FormulaData

sourceItemTransform - Variable in class net.sf.basedb.core.data.ItemListSyncFilterData

SourceItemTransform() - Constructor for enum class net.sf.basedb.core.SyncFilter.SourceItemTransform

SourceItemTransformer - Interface in net.sf.basedb.util.listable

Implementations are responsible for transforming a set of source item ID:s into a set of related target item ID:s.

SourceItemTransformerChain - Class in net.sf.basedb.util.listable

Chains together one or more source item transformers.

SourceItemTransformerChain(List<SourceItemTransformer>) - Constructor for class net.sf.basedb.util.listable.SourceItemTransformerChain

Create a new source item transformer chain.

SourceItemTransformerFactory - Interface in net.sf.basedb.util.listable

A source item transformer factory is responsible for creating SourceItemTransformer:s that can transform between the supported SourceItemTransformerFactory.getSupportedSourceItems(SyncFilter.SourceItemTransform) to the specified SourceItemTransformerFactory.getTargetItem().

SourceItemTransformerWithCache - Class in net.sf.basedb.util.listable

This is a wrapper transformer factory that can be applied to any other factory in order to provide support for caching.

SourceItemTransformerWithCache(SourceItemTransformerFactory) - Constructor for class net.sf.basedb.util.listable.SourceItemTransformerWithCache

Create a new source item transformer chain.

SourceItemTransformerWithCache(SourceItemTransformerFactory, String) - Constructor for class net.sf.basedb.util.listable.SourceItemTransformerWithCache

SourceItemTransformerWithCache.TransformerWithCache - Class in net.sf.basedb.util.listable

sourceItemType - Variable in class net.sf.basedb.core.data.ItemListSyncFilterData

sourceMustExist - Variable in class net.sf.basedb.core.data.ItemListSyncFilterData

sourcePlateMapper - Variable in class net.sf.basedb.plugins.PlateMappingImporter

sourceRowMapper - Variable in class net.sf.basedb.plugins.PlateMappingImporter

sources - Variable in class net.sf.basedb.core.data.BioMaterialEventData

sourceSubSetParameter - Variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

The bioAssays subset parameter.

sourceType - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

sourceType - Variable in class net.sf.basedb.util.listable.TransformCache.CacheKey

SPACE - Static variable in class net.sf.basedb.clients.web.util.HTML

spacingX - Variable in class net.sf.basedb.core.data.ArrayDesignBlockData

spacingX - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock

spacingY - Variable in class net.sf.basedb.core.data.ArrayDesignBlockData

spacingY - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock

spec - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn

specialLoggers - Variable in class net.sf.basedb.core.log.db.DbLogManagerFactory

SpecialQuery<C> - Class in net.sf.basedb.core

A special HQL query implementation that can return almost any kind of object.

SpecialQuery(String, String, String, Transformer<C, ?>) - Constructor for class net.sf.basedb.core.SpecialQuery

Specification() - Constructor for class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

specifications - Variable in class net.sf.basedb.util.annotations.InheritAnnotationsManager

specifications - Variable in class net.sf.basedb.util.annotations.RunnableInheritAnnotationsManager

spiParser - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo

splitHeader - Static variable in class net.sf.basedb.plugins.IlluminaRawDataImporter

A column header must be like: extendedpropertyname-arrayname

splitter - Variable in class net.sf.basedb.util.StreamCacher

splitValueWithUnit(String) - Static method in class net.sf.basedb.util.units.UnitUtil

Splits a value with an optional unit.

SPOT - Enum constant in enum class net.sf.basedb.core.ExtraValue.CoordinateType

The extra values are attached to spots.

SPOT - Enum constant in enum class net.sf.basedb.core.VirtualTable

Table that stores spot intensities for each spot in a data cube.

SPOT_ALL - Static variable in class net.sf.basedb.clients.web.ExperimentExplorer

Special value to use in the ExperimentExplorer.setPositionIndex(int) method to show all positions.

SPOT_AVG - Static variable in class net.sf.basedb.clients.web.ExperimentExplorer

Special value to use in the ExperimentExplorer.setPositionIndex(int) method to calculate the average for each bioassay.

SPOT_DATA - Static variable in class net.sf.basedb.core.File

The id for the FileType item representing a file containing analysed spot data.

SPOT_EXTRA_FLOAT - Enum constant in enum class net.sf.basedb.core.VirtualTable

Table that stores float spot extra values.

SPOT_EXTRA_INT - Enum constant in enum class net.sf.basedb.core.VirtualTable

Table that stores integer spot extra values.

SPOT_EXTRA_STRING - Enum constant in enum class net.sf.basedb.core.VirtualTable

Table that stores string spot extra values.

spotBatcher - Variable in class net.sf.basedb.core.BioAssaySet

The one and only spot batcher for this bioassayset.

spotBatcher - Variable in class net.sf.basedb.util.importer.spotdata.MatrixSpotIntensityEventHandler

spotBatcher - Variable in class net.sf.basedb.util.importer.spotdata.SerialSpotIntensityEventHandler

SpotBatcher - Class in net.sf.basedb.core

Batcher class for per-spot intensity values for bioassaysets.

SpotBatcher(DbControl, BioAssaySet) - Constructor for class net.sf.basedb.core.SpotBatcher

Create a new spot batcher for a bioassayset.

spotCount - Variable in class net.sf.basedb.util.export.spotdata.BfsExporter

spotCount - Variable in class net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter

spotCount - Variable in class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter

SpotData(int, float, float, int, MACalculator) - Constructor for class net.sf.basedb.plugins.MedianRatioNormalization.SpotData

SpotData(short, int, float, float, int, boolean, MACalculator) - Constructor for class net.sf.basedb.plugins.LowessNormalization.SpotData

SPOTDATA - Enum constant in enum class net.sf.basedb.core.Item

Representing spot data, not an actual item.

SpotExtraValueBatcher<I> - Class in net.sf.basedb.core

Batcher class for per-spot extra values.

SpotExtraValueBatcher(DbControl, ExtraValue) - Constructor for class net.sf.basedb.core.SpotExtraValueBatcher

Create a new spot batcher for a bioassayset.

spotExtraValueBatchers - Variable in class net.sf.basedb.core.BioAssaySet

Cache of already created spot extra value batchers.

spotFields - Variable in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

SpotIntensityParser - Interface in net.sf.basedb.util.importer.spotdata

A spot intensity parser is responsible for parsing and extracting spot intensity data on a row-by-row basis from a BASEfile.

spotIntensityParsers - Variable in class net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser

spotQuery - Variable in class net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter

spotQuery - Variable in class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter

spots - Variable in class net.sf.basedb.core.data.RawBioAssayData

spotSectionInfo - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo

SpotSectionInfo() - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo

Creates a new object.

spotSize - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter

spotSql - Variable in class net.sf.basedb.core.SpotBatcher

The statement that inserts spot data.

spotSqlStatement - Variable in class net.sf.basedb.core.SpotBatcher

The SQL string for the SpotBatcher.spotSql statement.

sql - Variable in class net.sf.basedb.core.AnnotationBatcher.InsertBatcher

sql - Variable in class net.sf.basedb.core.AnnotationBatcher.UpdateBatcher

sql - Variable in class net.sf.basedb.core.FastAnnotationLoader.FastIterator

sql - Variable in class net.sf.basedb.core.hibernate.ExecuteUpdateWork

sql - Variable in class net.sf.basedb.core.hibernate.ResultSetWork

SQL - Enum constant in enum class net.sf.basedb.core.query.QueryType

The query is using Structured Query Language.

SqlColumnExpression - Class in net.sf.basedb.core.query

An expression representing the column in a database tabe: alias.column.

SqlColumnExpression(String, String) - Constructor for class net.sf.basedb.core.query.SqlColumnExpression

sqlDeletes - Static variable in class net.sf.basedb.core.BatchUtil

Mapping classes/entity names to SQL deletes.

sqlInserts - Static variable in class net.sf.basedb.core.BatchUtil

Mapping classes/entity names to SQL inserts.

SqlQuery - Interface in net.sf.basedb.core.query

This is a query that is using SQL as the query language.

sqlResult - Variable in class net.sf.basedb.core.DynamicResultIterator

SqlResult - Interface in net.sf.basedb.core.query

This interface represents a single row in the results of a SqlQuery.

SqlResultImpl() - Constructor for class net.sf.basedb.core.DynamicResultIterator.SqlResultImpl

SqlResultIterator - Interface in net.sf.basedb.core.query

Return the result of a SqlQuery as an iterator.

SqlResultList<I> - Interface in net.sf.basedb.core.query

SqlStatement(String) - Constructor for class net.sf.basedb.core.hibernate.SchemaGenerator.SqlStatement

SqlStatement(String, String) - Constructor for class net.sf.basedb.core.hibernate.SchemaGenerator.SqlStatement

sqlSymbol - Variable in enum class net.sf.basedb.core.Operator

sqlType - Variable in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo

sqlType - Variable in class net.sf.basedb.core.hibernate.TypeWrapper

sqlType - Variable in class net.sf.basedb.core.PositionExtraValueBatcher

The sql type code of the value to insert.

sqlType - Variable in class net.sf.basedb.core.SpotExtraValueBatcher

The sql type code of the value to insert.

sqlTypeCode - Variable in class net.sf.basedb.core.BatchedPropertyInfo

sqlUpdates - Static variable in class net.sf.basedb.core.BatchUtil

Mapping classes/entity names to SQL updates.

sqrt - Variable in class net.sf.basedb.core.query.QuadraticMeanExpression

sqrt(Expression) - Static method in class net.sf.basedb.core.query.Expressions

Calculate the square root of an expression: new expression = sqrt(e).

SqrtExpression - Class in net.sf.basedb.core.query

SqrtExpression(Expression) - Constructor for class net.sf.basedb.core.query.SqrtExpression

squaredSum - Variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin

SquareRootConverter - Class in net.sf.basedb.util.jep.convert

Convert SquareRoot function to a Query API Expression.

SquareRootConverter() - Constructor for class net.sf.basedb.util.jep.convert.SquareRootConverter

sshFingerprint - Variable in class net.sf.basedb.core.data.FileServerData

sshFingerprint - Variable in class net.sf.basedb.util.uri.ConnectionParameters

sshPrivateKey - Variable in class net.sf.basedb.core.data.FileServerData

sshPrivateKey - Variable in class net.sf.basedb.util.uri.ConnectionParameters

sshPrivateKeyFormat - Variable in class net.sf.basedb.core.data.FileServerData

sshPrivateKeyFormat - Variable in class net.sf.basedb.util.uri.ConnectionParameters

sshPrivateKeyPassword - Variable in class net.sf.basedb.core.data.FileServerData

sshPrivateKeyPassword - Variable in class net.sf.basedb.util.uri.ConnectionParameters

ssl - Static variable in class net.sf.basedb.util.EmailUtil

SSLUtil2 - Class in net.sf.basedb.util.ssl

Utility class for working with SSL connections.

SSLUtil2() - Constructor for class net.sf.basedb.util.ssl.SSLUtil2

stacktrace - Variable in class net.sf.basedb.core.DbControl.State

stackTrace - Variable in class net.sf.basedb.core.data.JobData

stackTraceToImage(Throwable, int, int) - Static method in class net.sf.basedb.util.error.ThrowableUtil

Prints as much of a stacktrace as possible to an image.

stackTraceToString(Throwable) - Static method in class net.sf.basedb.util.error.ThrowableUtil

Convert a stacktrace to a string that is usually printed with the Throwable.printStackTrace() method.

StandardFieldConverter - Class in net.sf.basedb.util.export.spotdata

Default field converter implementation that works mainly by checking names and/or external id values of formulas, extra values, experimental factors etc.

StandardFieldConverter(DbControl, BioAssaySet) - Constructor for class net.sf.basedb.util.export.spotdata.StandardFieldConverter

Create a new standard field converter.

start - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream

start - Variable in class net.sf.basedb.util.ChainedProgressReporter

start() - Method in class net.sf.basedb.clients.jobagent.Agent

Start the job agent.

start() - Method in class net.sf.basedb.clients.web.extensions.service.DummyService

start() - Method in interface net.sf.basedb.clients.web.extensions.service.ServiceControllerAction

Start the service if it is not already running.

start() - Static method in class net.sf.basedb.core.Application

Starts the BASE application.

start() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

Called once before starting the import.

start() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter

Prepare for the import.

start(boolean) - Static method in class net.sf.basedb.core.Application

Deprecated.

In BASE 3.18; use Application.start(StartupOptions) instead

start(int) - Method in class net.sf.basedb.util.timer.PerformanceTimer

Start the timer with the given index.

start(String, String, String, JobAgent, Date) - Method in class net.sf.basedb.core.Job

Register the job as started.

start(String, String, JobAgent) - Method in class net.sf.basedb.core.Job

Register the job as started.

start(String, String, JobAgent, Date) - Method in class net.sf.basedb.core.Job

start(Application.StartupOptions) - Static method in class net.sf.basedb.core.Application

Starts the BASE application.

start(Extension<ServiceControllerAction>) - Static method in class net.sf.basedb.clients.web.extensions.service.Services

Start services as a result of an administrator has installed a new extension or updated/enabled an existing on.

startAgent() - Method in class net.sf.basedb.clients.jobagent.AgentController

Start the agent this controller is controlling.

startDate - Variable in class net.sf.basedb.core.data.NewsData

started - Variable in class net.sf.basedb.core.data.JobData

startIndex - Variable in class net.sf.basedb.core.FastAnnotationLoader.FastIterator

startJob(Job, JobAgentSettings) - Method in class net.sf.basedb.clients.jobagent.Agent

Start a job.

StartPageAction - Interface in net.sf.basedb.clients.web.extensions.startpage

Action for selecting the start page that should be displayed after logging in to BASE.

StartPageBean - Class in net.sf.basedb.clients.web.extensions.startpage

A simple bean-like implementation of the StartPageAction interface.

StartPageBean() - Constructor for class net.sf.basedb.clients.web.extensions.startpage.StartPageBean

StartRequestHandler - Class in net.sf.basedb.clients.jobagent.handlers

This is a request handler for the start command.

StartRequestHandler(Agent) - Constructor for class net.sf.basedb.clients.jobagent.handlers.StartRequestHandler

StartServiceRenderer - Class in net.sf.basedb.clients.web.extensions.service

A renderer that starts the service of a ServiceControllerAction.

StartServiceRenderer() - Constructor for class net.sf.basedb.clients.web.extensions.service.StartServiceRenderer

StartStopServlet - Class in net.sf.basedb.clients.web.servlet

Servlet listener for starting BASE when the web server is started and stopping BASE when the web server is stopped.

StartStopServlet() - Constructor for class net.sf.basedb.clients.web.servlet.StartStopServlet

startTime - Variable in class net.sf.basedb.clients.web.fileupload.FileUploadProgress

startTime - Variable in class net.sf.basedb.util.extensions.manager.ProcessResults

startTime - Variable in class net.sf.basedb.util.TransferRateProgressReporter

StartupOptions() - Constructor for class net.sf.basedb.core.Application.StartupOptions

startX - Variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin

state - Variable in class net.sf.basedb.core.DbControl

The state is holding Hibernate database connections and transaction.

state - Variable in class net.sf.basedb.core.log.EntityDetails

state - Variable in class net.sf.basedb.core.PluginRequest

state - Variable in class net.sf.basedb.core.PluginResponse

state - Variable in class net.sf.basedb.util.StaticCache.LockSafeInputStream

state - Variable in class net.sf.basedb.util.StaticCache.LockSafeOutputStream

State() - Constructor for class net.sf.basedb.core.DbControl.State

State(Closeable, StaticCache.LockEntry, boolean) - Constructor for class net.sf.basedb.util.StaticCache.State

stateless - Variable in class net.sf.basedb.core.AbstractHqlQuery

If the query should be executed in a stateless session or not.

statelessSession - Variable in class net.sf.basedb.core.AnnotationBatcher

StatelessSessionWrapper - Class in net.sf.basedb.core.hibernate

Wrapper around stateless Hibernate sessions that includes a query cache.

StatelessSessionWrapper(StatelessSession) - Constructor for class net.sf.basedb.core.hibernate.StatelessSessionWrapper

Creates a new session wrapper

statement - Variable in class net.sf.basedb.core.AnnotationBatcher.InsertBatcher

statement - Variable in class net.sf.basedb.core.AnnotationBatcher.UpdateBatcher

statements - Variable in class net.sf.basedb.core.hibernate.MultiUpdateWork

staticCache - Static variable in class net.sf.basedb.core.Application

Cache for static data.

StaticCache - Class in net.sf.basedb.util

A cache for storing data to files on the file system.

StaticCache(File) - Constructor for class net.sf.basedb.util.StaticCache

Creates a new static cache.

StaticCache.CleanupTask - Class in net.sf.basedb.util

A timer task that clean up the cache when it is executed.

StaticCache.LockEntry - Class in net.sf.basedb.util

Keeps track of a locked cached entry.

StaticCache.LockSafeInputStream - Class in net.sf.basedb.util

A lock-safe input stream that releases the associated read lock when the stream is closed.

StaticCache.LockSafeOutputStream - Class in net.sf.basedb.util

A lock-safe output stream that releases the associated write lock when the stream is closed.

StaticCache.State - Class in net.sf.basedb.util

Inner class for performing the actual release of locks and closing of streams (in/out).

StaticFilter<T> - Class in net.sf.basedb.util.filter

A filter implementation that either rejects or accepts all object (including null).

StaticFilter(boolean) - Constructor for class net.sf.basedb.util.filter.StaticFilter

Create a new filter.

StaticKeyManager - Class in net.sf.basedb.util.ssl

A key manager implementation that always selects a specified keystore entry.

StaticKeyManager(KeyStore, String, String) - Constructor for class net.sf.basedb.util.ssl.StaticKeyManager

Create a new key manager

staticRules - Static variable in class net.sf.basedb.util.overview.OverviewUtil

statistics - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup

status - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload

The status of the upload.

status - Variable in class net.sf.basedb.core.data.JobData

status - Variable in class net.sf.basedb.core.PluginResponse

status - Variable in class net.sf.basedb.util.extensions.manager.ProcessResults.FileResults

Status(boolean) - Constructor for enum class net.sf.basedb.core.plugin.Response.Status

Status(int, String, boolean) - Constructor for enum class net.sf.basedb.core.Job.Status

STATUS - Static variable in class net.sf.basedb.core.signal.Signal

The STATUS signal, that requests that the receiver should update the status on the system.

statusMessage - Variable in class net.sf.basedb.core.data.JobData

STDEV - Enum constant in enum class net.sf.basedb.util.plot.HistogramPlot.YAggregate

Plot the standard deviation of all y-values for spots falling into each bin.

steps - Variable in class net.sf.basedb.util.collections.MultiStepCollectionTransformer

sticky - Variable in class net.sf.basedb.core.data.NewsData

stickyCol - Variable in class net.sf.basedb.clients.web.taglib.table.Table

The id of a column that is "sticky".

stickyHeaders - Variable in class net.sf.basedb.clients.web.taglib.table.Table

If sticky headers is enabled or not.

stop() - Method in class net.sf.basedb.clients.jobagent.Agent

Stop the job agent.

stop() - Method in class net.sf.basedb.clients.web.extensions.service.DummyService

stop() - Method in interface net.sf.basedb.clients.web.extensions.service.ServiceControllerAction

Stop the service if it is running.

stop() - Method in class net.sf.basedb.core.Application.Pinger

Stop this pinger.

stop() - Static method in class net.sf.basedb.core.Application

Stops the BASE application.

stop(int) - Method in class net.sf.basedb.util.timer.PerformanceTimer

Stop a running timer.

stop(Extension<ServiceControllerAction>) - Static method in class net.sf.basedb.clients.web.extensions.service.Services

Start services as a result of an administrator has uninstalled an extension or is updating/disabling an existing on.

stopAgent() - Method in class net.sf.basedb.clients.jobagent.AgentController

Stop a running job agent by sending a stop request to the agents remote control service.

stopAll() - Method in class net.sf.basedb.util.timer.PerformanceTimer

Stop all running timers

stopPinger(Application.Pinger) - Static method in class net.sf.basedb.core.Application

StopRequestHandler - Class in net.sf.basedb.clients.jobagent.handlers

This is a request handler for the stop command.

StopRequestHandler(Agent) - Constructor for class net.sf.basedb.clients.jobagent.handlers.StopRequestHandler

Create a new stop request handler.

StopServiceRenderer - Class in net.sf.basedb.clients.web.extensions.service

A renderer that stops the service of a ServiceControllerAction.

StopServiceRenderer() - Constructor for class net.sf.basedb.clients.web.extensions.service.StopServiceRenderer

stopStart(int, int) - Method in class net.sf.basedb.util.timer.PerformanceTimer

Start one timer and stop another.

STORAGE_SIZE - Static variable in class net.sf.basedb.core.Quantity

The id for the Quantity object representing storage sizes.

storageType - Variable in class net.sf.basedb.core.data.BioPlateTypeData

store(String, Object, int) - Method in class net.sf.basedb.util.StaticCache

Store a serializable object in the cache.

store(TransformCache.CacheKey, Set<Integer>) - Method in class net.sf.basedb.util.listable.TransformCache

Store a new entry into the cache.

storeAttributes(ItemContext, String) - Method in class net.sf.basedb.util.extensions.ClientContext

Store all attributes that has been set on this context to the given ItemContext instance.

storeCurrentValuesAsOld(List<T>) - Method in class net.sf.basedb.core.data.ParameterValueData

Store the current values as old values, except if there are no current values or if old values have already been stored.

storePropertyFilters(Map<String, PropertyFilterData>) - Method in class net.sf.basedb.core.ItemContext

Store the current property filters and save them in the give filterData map.

storeValue(ParameterValues, Request, PluginParameter<T>) - Method in class net.sf.basedb.core.plugin.AbstractPlugin

Copy a parameter value from a Request to a ParameterValues object.

storeValue(ParameterValues, PluginParameter<T>, T) - Method in class net.sf.basedb.core.plugin.AbstractPlugin

Store a value in a ParameterValues object.

storeValues(ParameterValues, Request, PluginParameter<T>) - Method in class net.sf.basedb.core.plugin.AbstractPlugin

Copy a list of parameter values from a Request to a ParameterValues object.

strategy - Variable in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter

stream - Variable in class net.sf.basedb.util.StaticCache.State

stream() - Method in class net.sf.basedb.core.hibernate.QueryWrapper

StreamCacher - Class in net.sf.basedb.util

Caches the contents of a stream to a local temporary file.

StreamCacher(InputStream) - Constructor for class net.sf.basedb.util.StreamCacher

Create a new stream cacher for reading from the given master stream.

StreamCacher(InputStream, File) - Constructor for class net.sf.basedb.util.StreamCacher

Create a new stream cacher for reading from the given master stream.

StreamRedirector(Reader, Writer) - Constructor for class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor.StreamRedirector

streamtoword(byte[], int[]) - Static method in class net.sf.basedb.util.bcrypt.BCrypt

Cycically extract a word of key material

string(String) - Static method in class net.sf.basedb.core.query.Expressions

Create a constant expression from a string.

STRING - Enum constant in enum class net.sf.basedb.core.Type

String type where maximum length allowed is 255 characters.

STRING - Enum constant in enum class net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType

STRING - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper

STRING_TOO_LONG_ERROR - Static variable in class net.sf.basedb.plugins.util.Parameters

The name of the parameter created by Parameters.stringTooLongError(String, String, String, String...).

STRING_TYPE - Static variable in class net.sf.basedb.core.dbengine.TableInfo

StringConverter - Class in net.sf.basedb.util.extensions.debug

Convert strings to other data types.

StringConverter - Class in net.sf.basedb.util.jep.convert

Convert a String constant to a Query API Expression.

StringConverter() - Constructor for class net.sf.basedb.util.jep.convert.StringConverter

StringConverter(Type, Object) - Constructor for class net.sf.basedb.util.extensions.debug.StringConverter

StringDetector - Interface in net.sf.basedb.util.charset

Interface for checking if a text line in a file seems to be decoded correctly with the current character set.

StringFormatter - Class in net.sf.basedb.clients.web.formatter

Format a string for output on a web page.

StringFormatter() - Constructor for class net.sf.basedb.clients.web.formatter.StringFormatter

Create a new string formatter.

StringLengthComparator - Class in net.sf.basedb.util

A comparator implementation for strings that sorts them according to their length.

StringLengthComparator() - Constructor for class net.sf.basedb.util.StringLengthComparator

Create a new string length comparator instance.

stringMapping - Static variable in enum class net.sf.basedb.core.Type

stringMapping - Static variable in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section

StringMatcher - Class in net.sf.basedb.util.fuzzy

A wrapper class for fuzzy string matching using the SecondString package.

StringMatcher() - Constructor for class net.sf.basedb.util.fuzzy.StringMatcher

Create a new matcher using the default fuzzy matching algorithm: Level2JaroWinkler.

StringMatcher(StringDistance) - Constructor for class net.sf.basedb.util.fuzzy.StringMatcher

Create a new matcher using a specific fuzzy matching algorithm.

StringMatcher.FuzzyMatch - Class in net.sf.basedb.util.fuzzy

Wrapper that holds information about a fuzzy match.

StringParameterType - Class in net.sf.basedb.core

This class represent a parameter type that is a string.

StringParameterType() - Constructor for class net.sf.basedb.core.StringParameterType

Create a new string parameter type, setting the max length to 255 and nulls are allowed.

StringParameterType(Integer, String, boolean) - Constructor for class net.sf.basedb.core.StringParameterType

Create a new string parameter type.

StringParameterType(Integer, String, boolean, int, int, int) - Constructor for class net.sf.basedb.core.StringParameterType

StringParameterType(Integer, String, boolean, int, int, int, List<String>) - Constructor for class net.sf.basedb.core.StringParameterType

StringParameterType(Integer, String, boolean, int, int, int, Enumeration<String, String>) - Constructor for class net.sf.basedb.core.StringParameterType

StringParameterType(Integer, String, boolean, int, int, int, Enumeration<String, String>, boolean) - Constructor for class net.sf.basedb.core.StringParameterType

StringParameterValueData - Class in net.sf.basedb.core.data

String parameter value.

StringParameterValueData() - Constructor for class net.sf.basedb.core.data.StringParameterValueData

StringParameterValueData(String...) - Constructor for class net.sf.basedb.core.data.StringParameterValueData

stringTooLongError(String, String, String, String...) - Static method in class net.sf.basedb.plugins.util.Parameters

Create the parameter for handling too long strings.

stringTooLongErrorParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter

stringTooLongErrorParameter - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

StringTooLongException - Exception in net.sf.basedb.core

This exception is thrown when an item's field or a parameter which must be shorter than a specified length exceeds that length.

StringTooLongException() - Constructor for exception net.sf.basedb.core.StringTooLongException

Create a new StringTooLongException object.

StringTooLongException(String, String, int) - Constructor for exception net.sf.basedb.core.StringTooLongException

Create a new StringTooLongException object.

StringUtil - Class in net.sf.basedb.core

Utility methods that will make it easier to implement data validation for string attributes.

StringUtil() - Constructor for class net.sf.basedb.core.StringUtil

stringValue - Variable in enum class net.sf.basedb.core.Type

StringValue(String) - Constructor for class net.sf.basedb.util.excel.ExcelValue.StringValue

stripMarkup(CharSequence) - Static method in class net.sf.basedb.clients.web.util.HTML

Remove all HTML markup in a string and return what is left.

StylableTag - Class in net.sf.basedb.clients.web.taglib

Generic tag class for tags that want to support id, class and style of the main html object they use.

StylableTag(String) - Constructor for class net.sf.basedb.clients.web.taglib.StylableTag

Create a new stylable tag.

style - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

style - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

style - Variable in class net.sf.basedb.clients.web.extensions.login.FieldInfo

style - Variable in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

style - Variable in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean

style - Variable in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory

style - Variable in class net.sf.basedb.clients.web.extensions.section.SectionBean

style - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory

style - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory

style - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean

style - Variable in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean

style - Variable in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory

style - Variable in class net.sf.basedb.clients.web.taglib.menu.Menuseparator

Optional style attribute

style - Variable in class net.sf.basedb.clients.web.taglib.StylableTag

style - Variable in class net.sf.basedb.clients.web.taglib.tab.Tab

Optional style attribute

style - Variable in class net.sf.basedb.clients.web.taglib.table.Cell

Optional style attribute

style - Variable in class net.sf.basedb.clients.web.taglib.table.CellValue

styleCreator - Variable in class net.sf.basedb.clients.web.plugins.XlsxTemplate

styleCreator - Variable in class net.sf.basedb.util.excel.XlsxTableWriter

styles - Variable in class net.sf.basedb.clients.web.taglib.Head

A comma-separated list of stylesheets filenames.

styles - Variable in class net.sf.basedb.util.excel.CellStyleCreator

stylesheets - Variable in class net.sf.basedb.clients.web.extensions.AbstractJspFactory

stylesheets - Variable in class net.sf.basedb.clients.web.extensions.JspContext

Stylesheets - Class in net.sf.basedb.clients.web.taglib.extensions

Tag for creating <link> tags to stylesheets from a JspContext.

Stylesheets() - Constructor for class net.sf.basedb.clients.web.taglib.extensions.Stylesheets

subCategories - Variable in class net.sf.basedb.core.data.ItemSubtypeData

subCategoriesType - Variable in class net.sf.basedb.core.data.ItemSubtypeData

subCategory - Variable in class net.sf.basedb.core.data.ContextData

subCategory - Variable in class net.sf.basedb.core.ItemContext

subCategoryValues - Variable in class net.sf.basedb.core.data.AnnotationTypeCategoryData

subclass - Variable in class net.sf.basedb.clients.web.taglib.StylableTag

subclass - Variable in class net.sf.basedb.clients.web.taglib.table.Cell

More classes.

subcontext - Variable in class net.sf.basedb.clients.web.taglib.table.Table

subContext - Variable in class net.sf.basedb.core.ContextKey

subContext - Variable in class net.sf.basedb.core.data.ContextData

subContext - Variable in class net.sf.basedb.core.data.ContextIndex

subContext - Variable in class net.sf.basedb.core.data.JobData

subContext - Variable in class net.sf.basedb.core.ItemContext

subContext - Variable in class net.sf.basedb.core.plugin.GuiContext

SubContext - Class in net.sf.basedb.clients.web

Helper class for changing the current subcontext.

SubContext(String) - Constructor for class net.sf.basedb.clients.web.SubContext

Create an instance that doesn't change the current item context.

SubContext(String, ItemSubtype, AnnotationTypeCategory, ItemContext.AddFilter) - Constructor for class net.sf.basedb.clients.web.SubContext

Create an instance that changes the current item context.

SUBCONTEXT - Static variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemExtensionColumn

The named subcontext to use when using the extensions.

SUBDIR_FORMAT - Static variable in class net.sf.basedb.core.File

subdirectories - Variable in class net.sf.basedb.core.data.DirectoryData

subId - Variable in class net.sf.basedb.clients.web.taglib.menu.Submenu

The ID of the submenu.

subList(int, int) - Method in class net.sf.basedb.core.ItemResultList

Submenu - Class in net.sf.basedb.clients.web.taglib.menu

This tag defines a menu item inside a drop-down menu.

Submenu() - Constructor for class net.sf.basedb.clients.web.taglib.menu.Submenu

SUBMENU - Enum constant in enum class net.sf.basedb.clients.web.extensions.menu.MenuItemAction.MenuType

A menu item that opens a submenu.

submenuId - Variable in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

submenuId - Variable in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean

submenuId - Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

subquery - Variable in class net.sf.basedb.core.query.SubqueryExpression

SubqueryExpression - Class in net.sf.basedb.core.query

Expression that returns the result of a query as it's value.

SubqueryExpression(String, Query) - Constructor for class net.sf.basedb.core.query.SubqueryExpression

SUBSTANCE - Static variable in class net.sf.basedb.core.Quantity

The id for the Quantity object representing "amount of substance".

subtitle - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

subtitle - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

subtitle - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef

The subtitle of the column.

subtract(Expression, Expression) - Static method in class net.sf.basedb.core.query.Expressions

Subtract one expression from another: new expression = e1 - e2.

SubtractConverter - Class in net.sf.basedb.util.jep.convert

Convert Subtract function to a Query API Expression.

SubtractConverter() - Constructor for class net.sf.basedb.util.jep.convert.SubtractConverter

SubtractExpression - Class in net.sf.basedb.core.query

Subtract one expression from another: e1 - e2.

SubtractExpression(Expression, Expression) - Constructor for class net.sf.basedb.core.query.SubtractExpression

subTreeIterator - Variable in class net.sf.basedb.util.Tree.EntryIterator

An iterator over the subtree for each child of the root entry.

Subtypable - Interface in net.sf.basedb.core

A subtypable item is an item that can have a subtype.

SubtypableData - Interface in net.sf.basedb.core.data

A subtypable item is an item that can have a subtype.

subtypableItems - Static variable in class net.sf.basedb.core.Metadata

SubtypableRelatedItems - Annotation Interface in net.sf.basedb.core

Annotation that can be used by Subtypable items to tell about related items.

subtype - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

subtype - Variable in class net.sf.basedb.clients.web.extensions.list.SubtypeFilter

subtype - Variable in class net.sf.basedb.clients.web.SubContext

subtype - Variable in class net.sf.basedb.core.data.AnnotationTypeCategoryData

subtype - Variable in class net.sf.basedb.core.data.BioMaterialData

subtype - Variable in class net.sf.basedb.core.data.BioPlateTypeData

subtype - Variable in class net.sf.basedb.core.data.ContextData

subtype - Variable in class net.sf.basedb.core.data.DerivedBioAssayData

subtype - Variable in class net.sf.basedb.core.data.FileData

subtype - Variable in class net.sf.basedb.core.data.HardwareData

subtype - Variable in class net.sf.basedb.core.data.ItemListData

subtype - Variable in class net.sf.basedb.core.data.ItemListSyncFilterData

subtype - Variable in class net.sf.basedb.core.data.ItemSubtypeFileTypeData

subtype - Variable in class net.sf.basedb.core.data.JobData

subtype - Variable in class net.sf.basedb.core.data.KitData

subtype - Variable in class net.sf.basedb.core.data.PhysicalBioAssayData

subtype - Variable in class net.sf.basedb.core.data.ProtocolData

subtype - Variable in class net.sf.basedb.core.data.SoftwareData

subtype - Variable in class net.sf.basedb.core.data.TagData

subtype - Variable in class net.sf.basedb.core.Install.ItemSubtypeFT

subtype - Variable in class net.sf.basedb.core.ItemContext

subtype - Variable in class net.sf.basedb.util.annotations.InheritSpecification

subtype - Variable in class net.sf.basedb.util.bfs.MetadataModel

subtype - Variable in class net.sf.basedb.util.bfs.MetadataWriter

subtype - Variable in class net.sf.basedb.util.parser.DefaultItemFunction

SUBTYPE - Static variable in class net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter

SUBTYPE - Static variable in class net.sf.basedb.util.export.spotdata.MatrixBfsExporter

SUBTYPE - Static variable in class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter

SUBTYPE - Static variable in class net.sf.basedb.util.export.spotdata.SerialBfsExporter

subtypeColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

SubtypeFilter - Class in net.sf.basedb.clients.web.extensions.list

Filter implementation that accept (annotatable) items of a given subtype.

SubtypeFilter(ItemSubtype) - Constructor for class net.sf.basedb.clients.web.extensions.list.SubtypeFilter

subtypeId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Itemlist

subtypeId - Variable in class net.sf.basedb.core.MigrateRbaToDba.LineMapping

subtypeId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba

subtypeMapper - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

SubtypeMapping(File) - Constructor for class net.sf.basedb.core.MigrateRbaToDba.SubtypeMapping

subtypeName - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

subtypeQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

subtypes - Variable in class net.sf.basedb.clients.web.taglib.SubtypeSelector

SubtypeSelector - Class in net.sf.basedb.clients.web.taglib

This tag defines a selectable list of subtypes.

SubtypeSelector() - Constructor for class net.sf.basedb.clients.web.taglib.SubtypeSelector

successMessage - Variable in class net.sf.basedb.clients.web.plugins.SimpleExport

suffix - Variable in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerUtil

suffix - Variable in class net.sf.basedb.clients.web.extensions.renderer.PrefixSuffixRenderer

suffix - Variable in class net.sf.basedb.clients.web.taglib.table.CellValue

suffix - Static variable in class net.sf.basedb.core.Version

suffix - Variable in class net.sf.basedb.util.bfs.SequenceFilenameGenerator

suffix - Variable in class net.sf.basedb.util.formatter.PrefixSuffixFormatter

SuggestedFilenameGenerator - Class in net.sf.basedb.util.bfs

File name generator implementation that uses the suggested file name.

SuggestedFilenameGenerator() - Constructor for class net.sf.basedb.util.bfs.SuggestedFilenameGenerator

suggestedJobName - Variable in class net.sf.basedb.core.PluginResponse

sum - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup

sum - Variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin

sum(Expression) - Static method in class net.sf.basedb.core.query.Aggregations

Calculates the sum of all values of an expression: new expression = SUM(e)

SUM - Enum constant in enum class net.sf.basedb.util.plot.HistogramPlot.YAggregate

Plot the sum of all y-values for spots falling into each bin.

sumArrays(int[], int[]) - Static method in class net.sf.basedb.util.RemovableUtil

SumExpression - Class in net.sf.basedb.core.query

Calculates the sum of an expression: SUM(e)

SumExpression(Expression) - Constructor for class net.sf.basedb.core.query.SumExpression

summaries - Variable in class net.sf.basedb.core.DiskUsageStatistics

summary - Variable in class net.sf.basedb.util.extensions.manager.ProcessResults

Summary() - Constructor for class net.sf.basedb.core.DiskUsageStatistics.Summary

Summary(Group) - Constructor for class net.sf.basedb.core.DiskUsageStatistics.Summary

Summary(User) - Constructor for class net.sf.basedb.core.DiskUsageStatistics.Summary

summaryCache - Variable in class net.sf.basedb.clients.web.ExperimentExplorer

Caches annotation summaries.

SUPERVISOR - Static variable in class net.sf.basedb.core.Role

The id for the Role item representing supervisors.

supportColumnAliasInGroupBy() - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine

Returns FALSE.

supportColumnAliasInGroupBy() - Method in interface net.sf.basedb.core.dbengine.DbEngine

If the current database supports column aliases in the group by part of a query or not.

supportColumnAliasInGroupBy() - Method in class net.sf.basedb.core.dbengine.MySQLEngine

Returns TRUE.

supportColumnAliasInGroupBy() - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine

Returns TRUE.

supportColumnAliasInHaving() - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine

Returns FALSE.

supportColumnAliasInHaving() - Method in interface net.sf.basedb.core.dbengine.DbEngine

If the current database supports column aliases in the order by part of a query or not.

supportColumnAliasInHaving() - Method in class net.sf.basedb.core.dbengine.MySQLEngine

Returns TRUE.

supportColumnAliasInHaving() - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine

Returns FALSE.

supportColumnAliasInOrderBy() - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine

Returns FALSE.

supportColumnAliasInOrderBy() - Method in interface net.sf.basedb.core.dbengine.DbEngine

If the current database supports column aliases in the order by part of a query or not.

supportColumnAliasInOrderBy() - Method in class net.sf.basedb.core.dbengine.MySQLEngine

Returns TRUE.

supportColumnAliasInOrderBy() - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine

Returns TRUE.

supported - Variable in class net.sf.basedb.core.signal.AbstractSignalHandler

Holds the supported signals.

supported - Static variable in class net.sf.basedb.core.signal.ThreadSignalHandler

supports(String) - Method in class net.sf.basedb.core.PluginDefinition

Check if a plugin implements the interface specified by the plugin type.

supports(URI) - Method in interface net.sf.basedb.util.uri.ConnectionManagerFactory

Check if the given factory knows how to create a handler for the given URI.

supports(URI) - Method in class net.sf.basedb.util.uri.http.HttpConnectionManagerFactory

supports(PluginType) - Method in class net.sf.basedb.core.PluginDefinition

Check if a plugin implements the interface specified by the plugin type.

supports(Signal) - Method in class net.sf.basedb.core.signal.AbstractSignalHandler

supports(Signal) - Method in class net.sf.basedb.core.signal.DelegatingSignalHandler

Check if at least one handler has been registered for the given signal.

supports(Signal) - Method in interface net.sf.basedb.core.signal.SignalHandler

Check if a given signal is supported.

supportsAverage - Variable in enum class net.sf.basedb.core.Formula.Type

supportsAverage() - Method in enum class net.sf.basedb.core.Formula.Type

If a formula of this type can be used in an average expression or not.

supportsColumnAlias(DbEngine) - Method in enum class net.sf.basedb.core.query.QuerySection

If the current database supports column aliases in that part of the query.

supportsColumnAliasInWhere() - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine

Returns FALSE.

supportsColumnAliasInWhere() - Method in interface net.sf.basedb.core.dbengine.DbEngine

If the current database supports column aliases in the where part of a query or not.

supportsColumnAliasInWhere() - Method in class net.sf.basedb.core.dbengine.MySQLEngine

Returns FALSE.

supportsColumnAliasInWhere() - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine

Returns FALSE.

supportsConfigurations - Variable in class net.sf.basedb.core.data.PluginDefinitionData

supportsConfigurations() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport

supportsConfigurations() - Method in class net.sf.basedb.core.plugin.AbstractPlugin

Returns TRUE, since that is how the plugins used to work before this method was introduced.

supportsConfigurations() - Method in interface net.sf.basedb.core.plugin.Plugin

Return TRUE if the plugin supports different configurations when executing a job.

supportsConfigurations() - Method in class net.sf.basedb.core.PluginDefinition

Check if the plugin supports configurations or not when executing a job.

supportsConfigurations() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter

supportsConfigurations() - Method in class net.sf.basedb.plugins.Base1PluginExecuter

supportsConfigurations() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin

supportsConfigurations() - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

supportsConfigurations() - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

supportsConfigurations() - Method in class net.sf.basedb.plugins.BfsExporterPlugin

supportsConfigurations() - Method in class net.sf.basedb.plugins.CdfFileReporterImporter

supportsConfigurations() - Method in class net.sf.basedb.plugins.CloneReportersPlugin

supportsConfigurations() - Method in class net.sf.basedb.plugins.executor.AbstractIOSupport

supportsConfigurations() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

supportsConfigurations() - Method in class net.sf.basedb.plugins.FormulaFilter

supportsConfigurations() - Method in class net.sf.basedb.plugins.GalExporter

supportsConfigurations() - Method in class net.sf.basedb.plugins.HelpExporter

supportsConfigurations() - Method in class net.sf.basedb.plugins.HelpImporter

supportsConfigurations() - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter

supportsConfigurations() - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin

supportsConfigurations() - Method in class net.sf.basedb.plugins.JepExtraValueCalculator

supportsConfigurations() - Method in class net.sf.basedb.plugins.JepIntensityTransformer

supportsConfigurations() - Method in class net.sf.basedb.plugins.LowessNormalization

supportsConfigurations() - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator

supportsConfigurations() - Method in class net.sf.basedb.plugins.ManualTransformCreator

supportsConfigurations() - Method in class net.sf.basedb.plugins.MedianRatioNormalization

supportsConfigurations() - Method in class net.sf.basedb.plugins.PackedFileExporter

supportsConfigurations() - Method in class net.sf.basedb.plugins.PlateFlatFileImporter

supportsConfigurations() - Method in class net.sf.basedb.plugins.PlateMappingExporter

supportsConfigurations() - Method in class net.sf.basedb.plugins.PlateMappingImporter

supportsConfigurations() - Method in class net.sf.basedb.plugins.PluginConfigurationExporter

Always false

supportsConfigurations() - Method in class net.sf.basedb.plugins.PluginConfigurationImporter

supportsConfigurations() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter

supportsConfigurations() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter

supportsConfigurations() - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter

supportsConfigurations() - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter

supportsConfigurations() - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker

Returns FALSE.

supportsDeviceVerification - Variable in class net.sf.basedb.core.data.ClientData

supportsEncryption() - Method in interface net.sf.basedb.util.zip.FilePacker

Does the packer support encryption or not?

supportsEncryption() - Method in class net.sf.basedb.util.zip.ZipFilePacker

Encryption is supported.

supportsGetQuery() - Method in enum class net.sf.basedb.core.Item

Check if Item.getQuery() is supported by this item type.

supportsPushAnnotations(Item) - Static method in class net.sf.basedb.core.ItemSubtype

Check if the given item type has support for pushing annotations to the parent item or not.

SupportsPushAnnotations - Annotation Interface in net.sf.basedb.core

Annotation (java) that can be used by Subtypable items to enable/disable support for pushing annotations (BASE) to parent items.

supportUnits() - Method in class net.sf.basedb.core.AnnotationType

Checks if this annotation types support units.

symbol - Variable in class net.sf.basedb.core.data.ReporterData

symbol - Variable in class net.sf.basedb.core.data.UnitSymbolData

symbol - Variable in enum class net.sf.basedb.core.Operator

symbol - Variable in class net.sf.basedb.util.units.UnitCache.CacheKey

SYMBOL - Static variable in class net.sf.basedb.core.ClonableProperty

The property name of the "static" property ReporterData.getSymbol()

symbolColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

symbolMapper - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

symbols - Variable in class net.sf.basedb.core.data.QuantityData

symbols - Variable in class net.sf.basedb.core.data.UnitData

syncDate - Variable in class net.sf.basedb.core.data.ItemListData

SyncFilter - Class in net.sf.basedb.core

Holds information about a synchronization filter used by an item list.

SyncFilter(ItemListSyncFilterData) - Constructor for class net.sf.basedb.core.SyncFilter

SYNCFILTER - Enum constant in enum class net.sf.basedb.core.Item

The item is a SyncFilter

SyncFilter.SourceItemTransform - Enum Class in net.sf.basedb.core

syncFilters - Variable in class net.sf.basedb.core.data.ItemListData

synchronize(Set<Integer>, Set<Integer>) - Method in enum class net.sf.basedb.core.ItemList.SynchronizeOption

Synchronize the existing members with the items matching the current filter context.

synchronizeAllBioMaterialEvents() - Method in class net.sf.basedb.core.BioPlateEvent

Synchronize all properties on the child biomaterial events that are related to this event.

SynchronizedData(BfsParser) - Constructor for class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser.SynchronizedData

SynchronizedSpotDataParser - Class in net.sf.basedb.util.importer.spotdata

A parser that synchronizes the parsing of multiple underlying data parsers and a master reporter annotations parser.

SynchronizedSpotDataParser() - Constructor for class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser

Create a new synchronized data parser.

SynchronizedSpotDataParser.SynchronizedData - Class in net.sf.basedb.util.importer.spotdata

This class holds information that is sent to the event handler when SynchronizedSpotDataParser.DATA_EVENT:s are sent.

SynchronizeOption() - Constructor for enum class net.sf.basedb.core.ItemList.SynchronizeOption

synchronizeProperties(BioMaterialEventData, BioPlateEventParticipantData) - Method in class net.sf.basedb.core.BioPlateEvent

Synchronize all related properties between this event and the biomaterial event.

SYSTEM - Enum constant in enum class net.sf.basedb.core.Item

Not an item as susch.

systemCreated - Variable in class net.sf.basedb.core.Message

SystemData - Interface in net.sf.basedb.core.data

A system item is an item which has an additional id in the form of string.

systemId - Variable in class net.sf.basedb.core.data.BioPlateEventTypeData

systemId - Variable in class net.sf.basedb.core.data.DirectoryData

systemId - Variable in class net.sf.basedb.core.data.GroupData

systemId - Variable in class net.sf.basedb.core.data.ItemSubtypeData

systemId - Variable in class net.sf.basedb.core.data.QuantityData

systemId - Variable in class net.sf.basedb.core.data.QuotaData

systemId - Variable in class net.sf.basedb.core.data.QuotaTypeData

systemId - Variable in class net.sf.basedb.core.data.RoleData

systemId - Variable in class net.sf.basedb.core.data.UserData

systemIds - Static variable in class net.sf.basedb.core.SystemItems

A map from system id --> numeric id

SystemItem - Interface in net.sf.basedb.core

A SystemItem is an item which has an additional systemwide unique id in the form of string.

SystemItems - Class in net.sf.basedb.core

This class is used to map the system id of all SystemData items to the numerical internal id in the current installation.

SystemItems() - Constructor for class net.sf.basedb.core.SystemItems

systemPermissions - Variable in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring

systemPermissions - Variable in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring

T

t - Variable in class net.sf.basedb.util.extensions.logging.LogEntry

Tab - Class in net.sf.basedb.clients.web.taglib.tab

This tag defines the title and contents of a single tab inside a tab control.

Tab() - Constructor for class net.sf.basedb.clients.web.taglib.tab.Tab

Tab(InvokationContext<? super TabAction>) - Constructor for class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab

TabAction - Interface in net.sf.basedb.clients.web.extensions.tabcontrol

Action that inserts a new tab in a tabcontrol.

TabBean - Class in net.sf.basedb.clients.web.extensions.tabcontrol

A simple bean-like implementation of the TabAction interface.

TabBean() - Constructor for class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean

tabcontrol - Variable in class net.sf.basedb.clients.web.taglib.Help

The tabcontrol ID to get the help id from.

TabControl - Class in net.sf.basedb.clients.web.taglib.tab

This is the main tag for the tab control.

TabControl() - Constructor for class net.sf.basedb.clients.web.taglib.tab.TabControl

TabCrLfEncoderDecoder - Class in net.sf.basedb.util.encode

Symmetrical encoder/decoder implementation that replaces newline, carriage return, tab and backslash with \n, \r, \t and \\.

TabCrLfEncoderDecoder(boolean) - Constructor for class net.sf.basedb.util.encode.TabCrLfEncoderDecoder

Creates a new encoder/decoder.

tabIndex - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory

tabIndex - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory

tabIndex - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean

tabIndex - Variable in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean

tabIndex - Variable in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory

tabIndex - Variable in class net.sf.basedb.clients.web.taglib.Button

tabIndex - Variable in class net.sf.basedb.clients.web.taglib.Help

tabIndex - Variable in class net.sf.basedb.clients.web.taglib.Icon

tabIndex - Variable in class net.sf.basedb.clients.web.taglib.Input

tabIndex - Variable in class net.sf.basedb.clients.web.taglib.Select

tabIndex - Variable in class net.sf.basedb.clients.web.taglib.tab.Tab

tabIndex - Variable in class net.sf.basedb.clients.web.taglib.table.Button

tabIndex - Variable in class net.sf.basedb.clients.web.taglib.Zoom

table - Variable in class net.sf.basedb.clients.web.taglib.SubtypeSelector

table - Variable in class net.sf.basedb.clients.web.taglib.table.Cell

The parent <tbl:table> tag.

table - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef

The parent <tbl:table> tag.

table - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnHeaders

table - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnSubtitles

table - Variable in class net.sf.basedb.clients.web.taglib.table.Data

The parent <tbl:table> tag.

table - Variable in class net.sf.basedb.clients.web.taglib.table.Form

table - Variable in class net.sf.basedb.clients.web.taglib.table.Headers

table - Variable in class net.sf.basedb.clients.web.taglib.table.Hidden

The parent <tbl:table> tag.

table - Variable in class net.sf.basedb.clients.web.taglib.table.Label

The parent <tbl:table> tag.

table - Variable in class net.sf.basedb.clients.web.taglib.table.Navigator

The parent <tbl:table> tag.

table - Variable in class net.sf.basedb.clients.web.taglib.table.PresetSelector

The parent <tbl:table> tag.

table - Variable in class net.sf.basedb.clients.web.taglib.table.PropertyFilter

The parent <tbl:table> tag.

table - Variable in class net.sf.basedb.clients.web.taglib.table.Row

The parent <tbl:table> tag.

table - Variable in class net.sf.basedb.clients.web.taglib.table.Rows

table - Variable in class net.sf.basedb.core.BasicBatcher

The table where items of this type are stored.

table - Variable in class net.sf.basedb.core.dbengine.TableInfo

table - Variable in class net.sf.basedb.core.DynamicRestriction

table - Variable in class net.sf.basedb.core.hibernate.TableExistsWork

table - Variable in class net.sf.basedb.core.hibernate.TableInfoWork

table - Variable in class net.sf.basedb.core.query.VirtualColumnExpression

table - Variable in class net.sf.basedb.core.RawDataType

Table - Class in net.sf.basedb.clients.web.taglib.table

This is the main tag for the table.

Table() - Constructor for class net.sf.basedb.clients.web.taglib.table.Table

tableAlias - Variable in class net.sf.basedb.core.query.ReporterListExpression

tableColumn - Variable in class net.sf.basedb.core.query.ReporterListExpression

TableColumn - Class in net.sf.basedb.clients.web.taglib.table

Column properties class used to define table columns.
Example use in a jsp page:

TableColumn(String, String, String, Type, String, String, String, boolean, boolean, boolean, Formula.AverageMethod, Formatter<?>) - Constructor for class net.sf.basedb.clients.web.taglib.table.TableColumn

tableEncode(String) - Method in class net.sf.basedb.util.export.TableWriter

Encode the given string with the default encoder.

tableExists(String, Session) - Static method in class net.sf.basedb.core.HibernateUtil

Check if table in the dynamic database exists.

TableExistsWork - Class in net.sf.basedb.core.hibernate

A work implementation that checks if a given table exists in the database or not.

TableExistsWork(String, String, String) - Constructor for class net.sf.basedb.core.hibernate.TableExistsWork

Create a new work item.

TableInfo - Class in net.sf.basedb.core.dbengine

Holds minimal but useful information about a table in the database.

TableInfo(Table) - Constructor for class net.sf.basedb.core.dbengine.TableInfo

TableInfo(Table, DatabaseMetaData) - Constructor for class net.sf.basedb.core.dbengine.TableInfo

Deprecated.

In 3.14, use TableInfo(Table, DatabaseMetaData, String, String) instead

TableInfo(Table, DatabaseMetaData, String, String) - Constructor for class net.sf.basedb.core.dbengine.TableInfo

Create table info by reading JDBC metadata from the current database

TableInfo(Table, Dialect) - Constructor for class net.sf.basedb.core.dbengine.TableInfo

Create table info by reading the Hibernate mappings.

TableInfo.ColumnInfo - Class in net.sf.basedb.core.dbengine

Holds information about a single column in a table.

TableInfo.ForeignKeyInfo - Class in net.sf.basedb.core.dbengine

Holds information about a foreign key of a table.

TableInfo.IndexInfo - Class in net.sf.basedb.core.dbengine

Holds information about an index in a table.

TableInfo.PrimaryKeyInfo - Class in net.sf.basedb.core.dbengine

Holds information about the primary key of a table.

TableInfoWork - Class in net.sf.basedb.core.hibernate

A work implementation that loads database metadata for a table and returns it as a TableInfo object.

TableInfoWork(Table) - Constructor for class net.sf.basedb.core.hibernate.TableInfoWork

Create a new work item.

tableName - Variable in class net.sf.basedb.core.DropDynamicTableAction

tableName - Variable in class net.sf.basedb.core.RealTable

The unquoted table name.

tableName - Variable in enum class net.sf.basedb.core.Type

tableName - Variable in class net.sf.basedb.core.Update.DropColumnChange

tablePrintData(Object...) - Method in class net.sf.basedb.util.export.TableWriter

Print a data line to the parent writer using the default encoder and column formatters.

tablePrintData(EncoderDecoder, Object...) - Method in class net.sf.basedb.util.export.TableWriter

Print a data line to the parent writer.

tablePrintData(EncoderDecoder, Map<Integer, Formatter<?>>, Object...) - Method in class net.sf.basedb.util.excel.XlsxTableWriter

tablePrintData(EncoderDecoder, Map<Integer, Formatter<?>>, Object...) - Method in class net.sf.basedb.util.export.TableWriter

Print a data line to the parent writer.

tablePrintHeaders(Object...) - Method in class net.sf.basedb.util.excel.XlsxTableWriter

tablePrintHeaders(Object...) - Method in class net.sf.basedb.util.export.TableWriter

Print a header line to the parent writer.

TableWriter - Class in net.sf.basedb.util.export

Wraps a writer stream and provides methods for easier writing of tabular data.

TableWriter(Writer) - Constructor for class net.sf.basedb.util.export.TableWriter

Create a new table writer that is writing it's output to the given writer.

tabs - Variable in class net.sf.basedb.clients.web.taglib.tab.TabControl

The HTML for the tabs.

tag - Variable in class net.sf.basedb.core.data.ExtractData

tag - Variable in class net.sf.basedb.util.overview.validator.ExtractValidator.TagPosition

Tag - Class in net.sf.basedb.core

This class represents a tag.

Tag(TagData) - Constructor for class net.sf.basedb.core.Tag

TAG - Enum constant in enum class net.sf.basedb.core.Item

The item is a Tag.

TAG_REGEXP - Static variable in class net.sf.basedb.clients.web.util.HTML

This pattern can be used to fins HTML tags.

tagColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.ExtractImporter

TagData - Class in net.sf.basedb.core.data

This represents a tag that is used to mark an extract so that it can be tracked on physical bioassays.

TagData() - Constructor for class net.sf.basedb.core.data.TagData

tagElements - Variable in class net.sf.basedb.util.formatter.PropertyFilterFormatter

TAGGED_PARENT - Static variable in class net.sf.basedb.util.overview.Validator

Validator rule that checks if the parent to a non-tagged extract has a tag.

TagImporter - Class in net.sf.basedb.plugins.batchimport

Plug-in for importing tag items in a batch.

TagImporter() - Constructor for class net.sf.basedb.plugins.batchimport.TagImporter

TagLoader - Class in net.sf.basedb.util.overview.loader

Node loader implementation for tags.

TagLoader() - Constructor for class net.sf.basedb.util.overview.loader.TagLoader

tagMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter

TagPosition(Tag, int) - Constructor for class net.sf.basedb.util.overview.validator.ExtractValidator.TagPosition

tagQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

TagValidator - Class in net.sf.basedb.util.overview.validator

Validator implementation for tags.

TagValidator() - Constructor for class net.sf.basedb.util.overview.validator.TagValidator

takeOwnership() - Method in interface net.sf.basedb.core.Ownable

Take ownership of the item.

takeOwnership() - Method in class net.sf.basedb.core.OwnedItem

TAM - Enum constant in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.FormatType

tar - Variable in class net.sf.basedb.util.zip.TarFilePacker

TarFilePacker - Class in net.sf.basedb.util.zip

This class packs files into a TAR archive.

TarFilePacker() - Constructor for class net.sf.basedb.util.zip.TarFilePacker

Creates a new TarFilePacker.

TarFileUnpacker - Class in net.sf.basedb.plugins

A plugin for unpacking tar, gzipped tar and bzipped tar files to the BASE file system.

TarFileUnpacker() - Constructor for class net.sf.basedb.plugins.TarFileUnpacker

target - Variable in class net.sf.basedb.core.hibernate.DbIndexWork

target - Variable in class net.sf.basedb.util.listable.AbstractSourceItemTransformer

target - Variable in class net.sf.basedb.util.listable.AbstractSourceItemTransformerFactory

target - Variable in class net.sf.basedb.util.listable.SourceItemTransformerChain

TARGET - Enum constant in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section

targetIdMapper - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

targetItemIdColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

targetItemQueries - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

targetItemTypeColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

targetList - Variable in class net.sf.basedb.util.listable.TransformCache.CacheEntry

targetNotFoundErrorParameter - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

targets - Variable in class net.sf.basedb.core.AnyToAny.FastLinkLoader

targetType - Variable in class net.sf.basedb.clients.web.extensions.list.AnyLinkColumn

targetType - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

targetType - Variable in class net.sf.basedb.util.AnyToAnyLinkStatistics

targetType - Variable in class net.sf.basedb.util.listable.TransformCache.CacheKey

targetTypeMapper - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

TarUtil - Class in net.sf.basedb.util.zip

Contains utility functions for TAR archives.

TarUtil() - Constructor for class net.sf.basedb.util.zip.TarUtil

task - Variable in class net.sf.basedb.util.timer.ThreadTimerTask

tc - Variable in class net.sf.basedb.clients.web.taglib.tab.Tab

The parent TabControl object.

TEMPERATURE - Static variable in class net.sf.basedb.core.Quantity

The id for the Quantity object representing temperature.

TEMPLATE - Static variable in class net.sf.basedb.core.Directory

The id for the Directory item representing the template directory.

temporary - Variable in class net.sf.basedb.core.ItemContext.PropertyFilterPair

temporary - Variable in class net.sf.basedb.core.PropertyFilter

TEMPORARY - Enum constant in enum class net.sf.basedb.core.ItemContext.AddFilter

Add as temporary filter.

TEMPORARY - Static variable in class net.sf.basedb.core.PropertyFilter

Flag to use for temporary filters.

temporaryJoin(Join) - Method in class net.sf.basedb.core.AbstractQuery

temporaryJoins - Variable in class net.sf.basedb.core.AbstractQuery

Tempoarary joins, that are automatically cleared after each build.

temporarySelect(Select) - Method in class net.sf.basedb.core.AbstractQuery

temporarySelects - Variable in class net.sf.basedb.core.AbstractQuery

Tempoarary selections, that are automatically cleared after each build.

TempSeries(String, int, boolean) - Constructor for class net.sf.basedb.util.plot.HistogramPlot.TempSeries

testFixChildren() - Method in class net.sf.basedb.core.DerivedBioAssay

testIt(InputStream) - Method in class net.sf.basedb.util.charset.CharsetDetector

Test if the given input stream can be parsed with the configured character set.

testIt(InputStream, long, int) - Method in class net.sf.basedb.util.charset.CharsetDetector

Test if the given input stream can be parsed with the configured character set.

testTransactions() - Static method in class net.sf.basedb.core.HibernateUtil

TEXT - Enum constant in enum class net.sf.basedb.core.Type

Text blob type.

TEXT - Enum constant in enum class net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType

TEXT - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper

textarea - Variable in class net.sf.basedb.clients.web.taglib.Zoom

textLength(CharSequence) - Static method in class net.sf.basedb.clients.web.util.HTML

Counts the length of a string ignoring all characters in HTML markup tags.

TextParameterValueData - Class in net.sf.basedb.core.data

Text parameter value.

TextParameterValueData() - Constructor for class net.sf.basedb.core.data.TextParameterValueData

TextParameterValueData(String...) - Constructor for class net.sf.basedb.core.data.TextParameterValueData

TextWriter - Class in net.sf.basedb.core.migrate

Generic writer implementation that writes string values from a result set.

TextWriter(ResultSet, int, Writer, char[], char[][]) - Constructor for class net.sf.basedb.core.migrate.TextWriter

theAbstract - Variable in class net.sf.basedb.core.data.ExperimentData

theInstance - Static variable in class net.sf.basedb.util.jep.Log2Function

The one and only instance of this function.

thenMatch - Variable in class net.sf.basedb.util.charset.SimpleStringDetector

THERMAL_CONDUCTIVITY - Static variable in class net.sf.basedb.core.Quantity

The id for the Quantity object representing thermal conductivity.

thetaJoinConditions - Variable in class net.sf.basedb.core.AbstractQuery

Temporary list to hold theta join conditions if needed by the database.

thread - Variable in class net.sf.basedb.core.File.CharsetTesterThread

ThreadJobExecutor - Class in net.sf.basedb.clients.jobagent.executors

This is a job executor which executes jobs in the current thread.

ThreadJobExecutor() - Constructor for class net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor

ThreadJobExecutor.ShutdownHook - Class in net.sf.basedb.clients.jobagent.executors

ThreadSignalHandler - Class in net.sf.basedb.core.signal

An implementation of a signal handler that uses the Thread class to communicate signals back to the SignalTarget.

ThreadSignalHandler() - Constructor for class net.sf.basedb.core.signal.ThreadSignalHandler

Create a new thread signal handler.

ThreadSignalHandler(Thread) - Constructor for class net.sf.basedb.core.signal.ThreadSignalHandler

Create a new thread signal handler.

ThreadTimerTask - Class in net.sf.basedb.util.timer

Class for forcing the execution of a TimerTask in a new thread.

ThreadTimerTask(TimerTask, boolean) - Constructor for class net.sf.basedb.util.timer.ThreadTimerTask

Create a new threaded timer task.

throwable - Variable in class net.sf.basedb.util.ContextUtil.ContextResult

ThrowableUtil - Class in net.sf.basedb.util.error

Utility class for working with Throwable:s.

ThrowableUtil() - Constructor for class net.sf.basedb.util.error.ThrowableUtil

TICK_INTERVAL - Variable in class net.sf.basedb.core.Migration.ProgressInputStream

time - Variable in class net.sf.basedb.core.data.ChangeHistoryData

time - Variable in class net.sf.basedb.util.extensions.manager.ProcessResults.FileResults

TIME - Static variable in class net.sf.basedb.core.Quantity

The id for the Quantity object representing time.

timeout - Variable in class net.sf.basedb.clients.jobagent.AgentController

timeout - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload

The timeout in milliseconds that we wait for more data to arrive.

timeout - Variable in class net.sf.basedb.util.jobagent.JobAgentConnection

timeout - Variable in class net.sf.basedb.util.listable.TransformCache.CacheEntry

timeout - Variable in class net.sf.basedb.util.uri.http.HttpConnectionManager

timeoutChecker - Variable in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager

timeoutInMillis - Variable in class net.sf.basedb.util.listable.TransformCache

TimeoutTimer(HttpGet) - Constructor for class net.sf.basedb.util.uri.http.HttpConnectionManager.TimeoutTimer

timer - Variable in class net.sf.basedb.clients.web.extensions.service.DummyService

timer - Static variable in class net.sf.basedb.core.Application

The core timer which schedules events.

timer - Variable in class net.sf.basedb.util.timer.Scheduler

timers - Variable in class net.sf.basedb.util.timer.PerformanceTimer

timeSent - Variable in class net.sf.basedb.core.data.MessageData

timestamp - Variable in class net.sf.basedb.util.extensions.logging.LogEntry

TIMESTAMP - Enum constant in enum class net.sf.basedb.core.Type

The parameter is a date+time value.

TIMESTAMP - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper

TIMESTAMP_FORMAT - Static variable in class net.sf.basedb.core.DateUtil

TIMESTAMP_FORMAT_PARAMETER - Static variable in class net.sf.basedb.plugins.util.Parameters

The name of the parameter that is created by Parameters.timestampFormatParameter(String, String, String)

timestampFormat - Variable in class net.sf.basedb.core.migrate.postgres.PostgresResultWriterFactory

PostgreSQL uses 'yyyy-MM-dd HH:mm:ss' for timestamps.

timestampFormat - Variable in class net.sf.basedb.util.excel.AutoFormatter

timestampFormat - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil

timestampFormat - Variable in class net.sf.basedb.util.parser.FlatFileParser

The default timestamp format to use when creating mappers.

timestampFormatParameter(String, String, String) - Static method in class net.sf.basedb.plugins.util.Parameters

Parameter definition that asks for the format used by timestamp values when parsed from strings.

timestampFormatter - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

TimestampParameterType - Class in net.sf.basedb.core

This class represent a parameter type that is a timestamp.

TimestampParameterType() - Constructor for class net.sf.basedb.core.TimestampParameterType

Create a new timestamp parameter type, allowing null values.

TimestampParameterType(Date, boolean) - Constructor for class net.sf.basedb.core.TimestampParameterType

Create a new timestamp parameter type.

TimestampParameterType(Date, boolean, int, int, int, List<Date>) - Constructor for class net.sf.basedb.core.TimestampParameterType

Creates a new TimestampParameterType

TimestampParameterValueData - Class in net.sf.basedb.core.data

Date+time parameter value.

TimestampParameterValueData() - Constructor for class net.sf.basedb.core.data.TimestampParameterValueData

TimestampParameterValueData(Date...) - Constructor for class net.sf.basedb.core.data.TimestampParameterValueData

TimestampWriter - Class in net.sf.basedb.core.migrate

Generic writer implementation that writes timestamp values from a result set.

TimestampWriter(ResultSet, int, Writer, char[], FastDateFormat) - Constructor for class net.sf.basedb.core.migrate.TimestampWriter

title - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup

title - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

title - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

title - Variable in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

title - Variable in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean

title - Variable in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean

title - Variable in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean

title - Variable in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory

title - Variable in class net.sf.basedb.clients.web.extensions.section.SectionBean

title - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory

title - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory

title - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean

title - Variable in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean

title - Variable in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory

title - Variable in class net.sf.basedb.clients.web.plugins.ExportedProperty

title - Variable in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey

title - Variable in class net.sf.basedb.clients.web.taglib.Button

The title of the button.

title - Variable in class net.sf.basedb.clients.web.taglib.HideableSection

The title of the section.

title - Variable in class net.sf.basedb.clients.web.taglib.Input

An optional title.

title - Variable in class net.sf.basedb.clients.web.taglib.menu.Menuitem

The title of the menu item.

title - Variable in class net.sf.basedb.clients.web.taglib.menu.Submenu

The title of the menu item.

title - Variable in class net.sf.basedb.clients.web.taglib.Page

The title of the page.

title - Variable in class net.sf.basedb.clients.web.taglib.path.PathElement

The title of the menu item.

title - Variable in class net.sf.basedb.clients.web.taglib.tab.Tab

The title of the tab.

title - Variable in class net.sf.basedb.clients.web.taglib.table.Button

An optional title text on the button.

title - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef

The title of the column.

title - Variable in class net.sf.basedb.clients.web.taglib.table.Label

An optional title text on the button.

title - Variable in class net.sf.basedb.clients.web.taglib.table.Table

An optional title of the table.

title - Variable in class net.sf.basedb.clients.web.taglib.table.TableColumn

title - Variable in class net.sf.basedb.clients.web.taglib.Zoom

title - Variable in exception net.sf.basedb.clients.web.WebException

The title of the error message.

title - Static variable in class net.sf.basedb.core.Application

The title of the server.

title - Variable in class net.sf.basedb.core.data.ExperimentData

title - Variable in class net.sf.basedb.core.data.ReporterClonePropertyData

title - Variable in class net.sf.basedb.core.ExtendedProperty

title - Variable in class net.sf.basedb.core.IntensityFormula

title - Variable in class net.sf.basedb.core.RequestInformation

title - Variable in class net.sf.basedb.plugins.batchimport.FallbackIdMethod

title - Variable in class net.sf.basedb.plugins.batchimport.InternalIdMethod

title - Variable in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod

title - Variable in class net.sf.basedb.plugins.batchimport.PropertyIdMethod

title - Variable in class net.sf.basedb.util.export.spotdata.AnnotationAssayField

title - Variable in class net.sf.basedb.util.export.spotdata.AssayPropertyField

title - Variable in class net.sf.basedb.util.export.spotdata.JepDynamicField

title - Variable in class net.sf.basedb.util.export.spotdata.SimpleDynamicField

title - Variable in class net.sf.basedb.util.overview.Node

title - Variable in class net.sf.basedb.util.overview.Validator

title - Variable in enum class net.sf.basedb.util.parser.FlatFileParser.LineType

titlePrefix - Variable in class net.sf.basedb.util.overview.node.NameableNameGenerator

titleTemplate - Variable in class net.sf.basedb.clients.web.ModeInfo

tls - Static variable in class net.sf.basedb.util.EmailUtil

tmpTable - Variable in class net.sf.basedb.core.query.IdListRestriction

to - Variable in class net.sf.basedb.core.AnyToAny

to - Variable in class net.sf.basedb.core.data.MessageData

toAlpha - Variable in class net.sf.basedb.util.formatter.WellCoordinateFormatter

toArray() - Method in class net.sf.basedb.core.ItemResultList

toArray() - Method in class net.sf.basedb.util.Tree

Not supported.

toArray(Collection<T>, JsonConverter<? super T>) - Static method in class net.sf.basedb.util.json.JsonUtil

Convert a collection of objects to an array with JSON-compatible objects.

toArray(Iterator<T>, JsonConverter<? super T>) - Static method in class net.sf.basedb.util.json.JsonUtil

Convert all objects returned by the iterator to an array with JSON-compatible objects.

toArray(T[]) - Method in class net.sf.basedb.core.ItemResultList

toArray(T[]) - Method in class net.sf.basedb.util.Tree

Not supported.

ToBioSourceSourceItemTransformerFactory - Class in net.sf.basedb.util.listable

Transformer factory implementation for transforming to biosources.

ToBioSourceSourceItemTransformerFactory() - Constructor for class net.sf.basedb.util.listable.ToBioSourceSourceItemTransformerFactory

toChangeDetails(boolean, boolean) - Method in class net.sf.basedb.core.log.EntityDetails

Create a list of ChangeHistoryDetailData objects from the information in this object assuming that the entity is a subclass of BasicData.

toChangeDetails(Item, int, String, ChangeType, boolean, boolean) - Method in class net.sf.basedb.core.log.EntityDetails

Create a list of ChangeHistoryDetailData objects using a mix of the information in this object, and the given parameters.

toChangeHistoryData() - Method in class net.sf.basedb.core.log.TransactionDetails

Convert the information about the transaction to a ChangeHistoryData object.

toData() - Method in class net.sf.basedb.core.ClonableProperty

Create a data-layer reprsentation of the cloned property.

toDate(Expression) - Static method in class net.sf.basedb.core.query.Expressions

Get the date part from a date or timestamp expression.

ToDateExpression - Class in net.sf.basedb.core.query

Get the date part of a date or timestamp epxression.

ToDateExpression(Expression) - Constructor for class net.sf.basedb.core.query.ToDateExpression

ToDerivedBioAssaySourceItemTransformerFactory - Class in net.sf.basedb.util.listable

Transformer factory implementation for transforming to derived bioassays.

ToDerivedBioAssaySourceItemTransformerFactory() - Constructor for class net.sf.basedb.util.listable.ToDerivedBioAssaySourceItemTransformerFactory

toDescription() - Method in class net.sf.basedb.clients.web.extensions.ServletWrapperKey

toDescription() - Method in class net.sf.basedb.util.extensions.manager.ExtensionKey

toDescription() - Method in class net.sf.basedb.util.extensions.manager.ExtensionPointKey

toDescription() - Method in class net.sf.basedb.util.extensions.manager.FactoryParametersKey

toDescription() - Method in interface net.sf.basedb.util.extensions.manager.ObjectKey

Get a string description of the key that is suitable for use in (error) messages to users.

toDescription() - Method in class net.sf.basedb.util.extensions.manager.PluginInfoKey

toExcelValue(Boolean) - Method in class net.sf.basedb.util.formatter.BooleanFormatter

toExcelValue(Integer) - Method in class net.sf.basedb.util.formatter.WellCoordinateFormatter

toExcelValue(Number) - Method in class net.sf.basedb.util.formatter.AdaptiveNumberFormatter

toExcelValue(Number) - Method in class net.sf.basedb.util.formatter.IntegerFormatter

toExcelValue(Number) - Method in class net.sf.basedb.util.formatter.NumberFormatFormatter

toExcelValue(Number) - Method in class net.sf.basedb.util.formatter.NumberFormatter

toExcelValue(Object) - Method in class net.sf.basedb.util.excel.AutoFormatter

toExcelValue(Object) - Method in class net.sf.basedb.util.formatter.MultiFormatter

toExcelValue(String) - Method in class net.sf.basedb.clients.web.formatter.NiceFormatter

No escaping is needed.

toExcelValue(String) - Method in class net.sf.basedb.clients.web.formatter.StringFormatter

No escaping is needed.

toExcelValue(Date) - Method in class net.sf.basedb.util.formatter.DateFormatter

toExcelValue(T) - Method in interface net.sf.basedb.util.excel.ExcelFormatter

Convert and format the given value to an Excel value.

toExcelValue(T) - Method in class net.sf.basedb.util.excel.WrappedFormatter

toExcelValue(T) - Method in class net.sf.basedb.util.formatter.ToStringFormatter

toExpression(Integer) - Method in class net.sf.basedb.util.jep.convert.IntegerConverter

Convert to expression by calling Expressions.integer(int).

toExpression(Number) - Method in class net.sf.basedb.util.jep.convert.FloatConverter

Convert to expression by calling Expressions.aFloat(float).

toExpression(String) - Method in class net.sf.basedb.util.jep.convert.StringConverter

Convert to expression by calling Expressions.string(String).

toExpression(ASTConstant) - Method in class net.sf.basedb.util.jep.convert.ASTConstantConverter

Get the value from the constant node and check the ConverterFactory for a registered converter for the class and use it.

toExpression(ASTFunNode) - Method in class net.sf.basedb.util.jep.convert.ASTFunNodeConverter

Get the PostfixMathCommandI object from the function node and delegate conversion to JepExpressionFunction if that interface is implemented.

toExpression(ASTVarNode) - Method in class net.sf.basedb.util.jep.convert.ASTVarNodeConverter

Converts a JEP variable to a parameter.

toExpression(Node) - Method in class net.sf.basedb.util.jep.ChannelFunction

Use the Dynamic.column(VirtualColumn) method to create an expression referencing a channel intensity.

toExpression(Node) - Method in class net.sf.basedb.util.jep.convert.AbsConverter

Convert to expression by calling Expressions.abs(Expression).

toExpression(Node) - Method in class net.sf.basedb.util.jep.convert.AddConverter

Convert to expression by calling Expressions.add(Expression, Expression).

toExpression(Node) - Method in class net.sf.basedb.util.jep.convert.DivideConverter

Convert to expression by calling Expressions.divide(Expression, Expression).

toExpression(Node) - Method in class net.sf.basedb.util.jep.convert.ExpConverter

Convert to expression by calling Expressions.exp(Expression).

toExpression(Node) - Method in class net.sf.basedb.util.jep.convert.IfConverter

Convert to expression by calling Expressions.caseWhen(Expression, net.sf.basedb.core.query.WhenStatement[]).

toExpression(Node) - Method in class net.sf.basedb.util.jep.convert.LogarithmConverter

Convert to expression by calling Expressions.log10(Expression).

toExpression(Node) - Method in class net.sf.basedb.util.jep.convert.MultiplyConverter

Convert to expression by calling Expressions.multiply(Expression, Expression).

toExpression(Node) - Method in class net.sf.basedb.util.jep.convert.NaturalLogarithmConverter

Convert to expression by calling Expressions.ln(Expression).

toExpression(Node) - Method in class net.sf.basedb.util.jep.convert.SquareRootConverter

Convert to expression by calling Expressions.sqrt(Expression).

toExpression(Node) - Method in class net.sf.basedb.util.jep.convert.SubtractConverter

Convert to expression by calling Expressions.subtract(Expression, Expression).

toExpression(Node) - Method in class net.sf.basedb.util.jep.convert.UMinusConverter

toExpression(Node) - Method in class net.sf.basedb.util.jep.ExtraValueFunction

Use the Dynamic.extraValue(ExtraValue) method to create an expression referencing an extra value.

toExpression(Node) - Method in interface net.sf.basedb.util.jep.JepExpressionFunction

Convert this function to an Expression that can be used in a query.

toExpression(Node) - Method in class net.sf.basedb.util.jep.Log2Function

Use the Expressions.log2(Expression) method to create an expression taking the 2-based logarithm of the argument.

toExpression(Node) - Method in class net.sf.basedb.util.jep.MeanFunction

Use the Dynamic.meanRawData(String) method to create an expression for the mean of the given raw data property.

toExpression(Node) - Method in class net.sf.basedb.util.jep.PositionFunction

Use the Dynamic.column(VirtualColumn) method to create an expression referencing a position.

toExpression(Node) - Method in class net.sf.basedb.util.jep.RawChannelFunction

Use the Dynamic.column(VirtualColumn) method to create an expression referencing a channel intensity.

toExpression(Node) - Method in class net.sf.basedb.util.jep.RawFunction

Use the Dynamic.rawData(String) method to create an expression referencing a raw data property.

toExpression(Node) - Method in class net.sf.basedb.util.jep.ReporterFunction

Use the Dynamic.reporter(String) method to create an expression referencing a reporter property.

toExpression(Node) - Method in class net.sf.basedb.util.jep.ScoreFunction

Use the Dynamic.score(ReporterList) method to create an expression referencing the score of a reporter in the reporter list.

toExpression(T) - Method in class net.sf.basedb.util.jep.convert.AbstractJepConversionFunction

Convert to a restriction and then use Expressions.bool(Restriction) to create a boolean expression.

toExpression(T) - Method in interface net.sf.basedb.util.jep.convert.JepConversionFunction

Convert the object to an expression.

ToExtractSourceItemTransformerFactory - Class in net.sf.basedb.util.listable

Transformer factory implementation for transforming to extracts.

ToExtractSourceItemTransformerFactory() - Constructor for class net.sf.basedb.util.listable.ToExtractSourceItemTransformerFactory

ToExtractSourceItemTransformerFactory(boolean) - Constructor for class net.sf.basedb.util.listable.ToExtractSourceItemTransformerFactory

toFile(String) - Method in class net.sf.basedb.util.extensions.manager.Settings

A file is typically stored under the absolute path, but if it matches the plug-ins directory we replace it with {plugins.dir}.

toHex(Color) - Static method in class net.sf.basedb.util.ColorGenerator

Generate a hex color string from a Color object.

toId - Variable in class net.sf.basedb.core.data.AnyToAnyData

toInt(Set<Include>) - Static method in enum class net.sf.basedb.core.Include

token - Variable in class net.sf.basedb.core.data.UserDeviceData

tokenize(String, String, boolean) - Static method in class net.sf.basedb.core.StringUtil

Tokenize a string by splitting it at positions matching the regular expression, optionally ignoring matches that are inside quotes.

tokenize(String, String, boolean, boolean) - Static method in class net.sf.basedb.core.StringUtil

Tokenize a string by splitting it at positions matching the regular expression.

toKey(File) - Method in class net.sf.basedb.util.extensions.manager.Settings

A file is typically stored under the absolute path, but if it matches the plug-ins directory we replace it with {plugins.dir}.

toLoggableString(Type, Object) - Static method in class net.sf.basedb.core.log.EntityDetails

toMd5(SortedSet<Integer>) - Static method in class net.sf.basedb.core.SyncFilter

Calculate the MD5 sum of all all ID values in the collection.

TOOL - Enum constant in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section

toolbar - Variable in class net.sf.basedb.clients.web.taglib.table.Button

The parent <tbl:toolbar> tag.

toolbar - Variable in class net.sf.basedb.clients.web.taglib.table.Label

The parent <tbl:toolbar> tag.

Toolbar - Class in net.sf.basedb.clients.web.taglib.table

This tag creates a toolbar.

Toolbar() - Constructor for class net.sf.basedb.clients.web.taglib.table.Toolbar

TOOLBAR_ITEMS - Static variable in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil

An array containing all items that we are registering an extension point for.

ToolbarButtonRenderer - Class in net.sf.basedb.clients.web.extensions.toolbar

A renderer for toolbar button actions, which displays the action as a toolbar button.

ToolbarButtonRenderer() - Constructor for class net.sf.basedb.clients.web.extensions.toolbar.ToolbarButtonRenderer

Create a new "standalone" toolbar button renderer.

ToolbarButtonRenderer(JspContext) - Constructor for class net.sf.basedb.clients.web.extensions.toolbar.ToolbarButtonRenderer

Create a new toolbar button renderer.

ToolbarButtonRendererFactory - Class in net.sf.basedb.clients.web.extensions.toolbar

Factory that create ToolbarButtonRenderer objects for rendering ButtonAction:s.

ToolbarButtonRendererFactory() - Constructor for class net.sf.basedb.clients.web.extensions.toolbar.ToolbarButtonRendererFactory

ToolbarUtil - Class in net.sf.basedb.clients.web.extensions.toolbar

Utility class for toolbar extension points.

ToolbarUtil() - Constructor for class net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil

toolParameters - Variable in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator

toolParameters - Variable in class net.sf.basedb.plugins.ManualTransformCreator

tooltip - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

tooltip - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

tooltip - Variable in class net.sf.basedb.clients.web.extensions.login.FieldInfo

tooltip - Variable in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

tooltip - Variable in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean

tooltip - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory

tooltip - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory

tooltip - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean

tooltip - Variable in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean

tooltip - Variable in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory

tooltip - Variable in class net.sf.basedb.clients.web.taglib.Button

An optional tooltip.

tooltip - Variable in class net.sf.basedb.clients.web.taglib.Help

Optional tooltip.

tooltip - Variable in class net.sf.basedb.clients.web.taglib.Icon

An optional tooltip.

tooltip - Variable in class net.sf.basedb.clients.web.taglib.menu.Menuitem

A tooltip explaining the menu item.

tooltip - Variable in class net.sf.basedb.clients.web.taglib.menu.Submenu

A tooltip explaining the menu item.

tooltip - Variable in class net.sf.basedb.clients.web.taglib.path.PathElement

A tooltip explaining the link.

tooltip - Variable in class net.sf.basedb.clients.web.taglib.PropertyValue

An optional tooltip.

tooltip - Variable in class net.sf.basedb.clients.web.taglib.tab.Tab

A popup tooltip text.

tooltip - Variable in class net.sf.basedb.clients.web.taglib.table.Button

An optional tooltip that will show when the mouse is over the button.

tooltip - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef

A tooltip with explaining text.

tooltip - Variable in class net.sf.basedb.clients.web.taglib.table.Label

An optional tooltip that will show when the mouse is over the button.

tooltip - Variable in class net.sf.basedb.clients.web.taglib.Zoom

Optional tooltip.

tooManyValuesErrorParameter - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

TOP - Static variable in class net.sf.basedb.clients.web.taglib.tab.TabControl

Tabs are at the top of the tab control.

ToPhysicalBioAssaySourceItemTransformerFactory - Class in net.sf.basedb.util.listable

Transformer factory implementation for transforming to physical bioassays.

ToPhysicalBioAssaySourceItemTransformerFactory() - Constructor for class net.sf.basedb.util.listable.ToPhysicalBioAssaySourceItemTransformerFactory

toPluginParameter(DbControl, BioAssaySet) - Method in class net.sf.basedb.plugins.executor.ParameterDefinition

Convert this parameter definition to a PluginParameter object.

toQl(DbControl) - Method in class net.sf.basedb.core.AbstractQuery

toQl(DbControl) - Method in interface net.sf.basedb.core.query.Query

Generate the query string that is going to be sent to the underlying query system (eg.

toQl(Query, DbControl) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.InExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.AnnotationRestriction

toQl(Query, DbControl) - Method in class net.sf.basedb.core.AnnotationSet.ProjectSpecificAnnotationsRestriction

toQl(Query, DbControl) - Method in class net.sf.basedb.core.DynamicJoin

toQl(Query, DbControl) - Method in class net.sf.basedb.core.DynamicRestriction

toQl(Query, DbControl) - Method in class net.sf.basedb.core.ExtraValueExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.ExtraValueJoin

toQl(Query, DbControl) - Method in class net.sf.basedb.core.MeanRawDataPropertyExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.AbsExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.AddExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.AndRestriction

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.AnnotationJoin

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.AnyToAnyRestriction

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.AscOrder

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.BetweenRestriction

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.BooleanExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.CaseExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.ConditionalQueryElement

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.CountExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.DescOrder

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.DivideExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.EqRestriction

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.ExpExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.ExpressionSelect

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.FloatExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.GeometricMeanExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.GteqRestriction

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.GtRestriction

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlElementsExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlEntityExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlEntityParameterExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlIndexExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlInnerJoin

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlLeftJoin

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlPropertyExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlRightJoin

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlSizeExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.IdListRestriction

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.InRestriction

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.IntegerExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.LikeRestriction

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.LogExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.LteqRestriction

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.LtRestriction

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.MaxExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.MeanExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.MinExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.MultiplyExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.NegateExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.NeqRestriction

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.NotRestriction

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.OrRestriction

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.ParameterExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.PermissionRestriction

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.PowerExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.QuadraticMeanExpression

toQl(Query, DbControl) - Method in interface net.sf.basedb.core.query.QueryElement

Create a query language string of the query element.

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.ReporterListExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.RlikeRestriction

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.SelectedExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.SharedToRestriction

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.SqlColumnExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.SqrtExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.SubqueryExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.SubtractExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.SumExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.ToDateExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.VirtualColumnExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.VirtualColumnExpression.WrappedExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.RawBioAssayPropertyExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.RawDataPropertyExpression

toQl(Query, DbControl) - Method in class net.sf.basedb.core.RealJoin

toQl(Query, DbControl) - Method in class net.sf.basedb.core.ReporterListJoin

toQl(Query, DbControl) - Method in class net.sf.basedb.core.ReporterPropertyExpression

ToRawBioAssaySourceItemTransformerFactory - Class in net.sf.basedb.util.listable

Transformer factory implementation for transforming to raw bioassays.

ToRawBioAssaySourceItemTransformerFactory() - Constructor for class net.sf.basedb.util.listable.ToRawBioAssaySourceItemTransformerFactory

toReferenceUnit(double) - Method in class net.sf.basedb.core.Unit

Convert a value from this unit to the reference unit.

toRestriction(ASTFunNode) - Method in class net.sf.basedb.util.jep.convert.ASTFunNodeConverter

Get the PostfixMathCommandI object from the function node and delegate conversion to JepRestrictionFunction if that interface is implemented.

toRestriction(Node) - Method in class net.sf.basedb.util.jep.convert.AndConverter

Convert to restriction by calling Restrictions.and(Restriction[]).

toRestriction(Node) - Method in class net.sf.basedb.util.jep.convert.EqualsConverter

Convert to restriction by calling Restrictions.eq(Expression, Expression).

toRestriction(Node) - Method in class net.sf.basedb.util.jep.convert.GreaterConverter

Convert to restriction by calling Restrictions.gt(net.sf.basedb.core.query.Expression, net.sf.basedb.core.query.Expression).

toRestriction(Node) - Method in class net.sf.basedb.util.jep.convert.GreaterEqualsConverter

Convert to restriction by calling Restrictions.gteq(net.sf.basedb.core.query.Expression, net.sf.basedb.core.query.Expression).

toRestriction(Node) - Method in class net.sf.basedb.util.jep.convert.LessConverter

Convert to restriction by calling Restrictions.lt(net.sf.basedb.core.query.Expression, net.sf.basedb.core.query.Expression).

toRestriction(Node) - Method in class net.sf.basedb.util.jep.convert.LessEqualsConverter

Convert to restriction by calling Restrictions.lteq(net.sf.basedb.core.query.Expression, net.sf.basedb.core.query.Expression).

toRestriction(Node) - Method in class net.sf.basedb.util.jep.convert.NotConverter

Convert to restriction by calling Restrictions.not(Restriction).

toRestriction(Node) - Method in class net.sf.basedb.util.jep.convert.NotEqualsConverter

Convert to restriction by calling Restrictions.neq(net.sf.basedb.core.query.Expression, net.sf.basedb.core.query.Expression).

toRestriction(Node) - Method in class net.sf.basedb.util.jep.convert.OrConverter

Convert to restriction by calling Restrictions.or(Restriction[]).

toRestriction(Node) - Method in class net.sf.basedb.util.jep.InReporterListFunction

Use the Dynamic.isPartOf(ReporterList) method to create a restriction checking that a reporter is found in the reporter list.

toRestriction(Node) - Method in interface net.sf.basedb.util.jep.JepRestrictionFunction

Convert this function to a Restriction that can be used in a query.

toRestriction(Node) - Method in class net.sf.basedb.util.jep.NotInReporterListFunction

Use the Dynamic.isNotPartOf(ReporterList) method to create a restriction checking that a reporter isn't found in the reporter list.

toRestriction(T) - Method in class net.sf.basedb.util.jep.convert.AbstractJepConversionFunction

toRestriction(T) - Method in interface net.sf.basedb.util.jep.convert.JepConversionFunction

Convert the object to a restriction.

TORGUE - Static variable in class net.sf.basedb.core.Quantity

The id for the Quantity object representing torque.

ToSampleSourceItemTransformerFactory - Class in net.sf.basedb.util.listable

Transformer factory implementation for transforming to samples.

ToSampleSourceItemTransformerFactory() - Constructor for class net.sf.basedb.util.listable.ToSampleSourceItemTransformerFactory

ToSampleSourceItemTransformerFactory(boolean) - Constructor for class net.sf.basedb.util.listable.ToSampleSourceItemTransformerFactory

ToSpaceEncoderDecoder - Class in net.sf.basedb.util.encode

Encoder implementation that replaces newline, carriage return, tab and backslash with a space.

ToSpaceEncoderDecoder() - Constructor for class net.sf.basedb.util.encode.ToSpaceEncoderDecoder

toString() - Method in class net.sf.basedb.clients.jobagent.slotmanager.Slot

toString() - Method in class net.sf.basedb.clients.web.extensions.service.DummyService

toString() - Method in class net.sf.basedb.clients.web.extensions.ServletWrapperKey

toString() - Method in class net.sf.basedb.clients.web.extensions.skin.ImageRemapper

toString() - Method in class net.sf.basedb.clients.web.ModeInfo.ModeContext

toString() - Method in class net.sf.basedb.clients.web.ModeInfo

toString() - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey

toString() - Method in class net.sf.basedb.core.AbstractQuery

toString() - Method in class net.sf.basedb.core.AnnotationBetweenRestriction

toString() - Method in class net.sf.basedb.core.authentication.AuthenticationMethod

toString() - Method in class net.sf.basedb.core.BasicItem

toString() - Method in enum class net.sf.basedb.core.BioMaterialEvent.Type

toString() - Method in enum class net.sf.basedb.core.BioWell.LockMode

toString() - Method in class net.sf.basedb.core.BlockInfo

Get the coordinate as [number;metaGridX,metaGridY]

toString() - Method in class net.sf.basedb.core.BooleanParameterType

toString() - Method in class net.sf.basedb.core.ClonableProperty

toString() - Method in class net.sf.basedb.core.data.BasicData

The string will look like ClassName[id=55] or ClassName[new].

toString() - Method in class net.sf.basedb.core.data.BooleanParameterValueData

toString() - Method in class net.sf.basedb.core.data.DateParameterValueData

toString() - Method in class net.sf.basedb.core.data.DoubleParameterValueData

toString() - Method in class net.sf.basedb.core.data.FloatParameterValueData

toString() - Method in class net.sf.basedb.core.data.IntegerParameterValueData

toString() - Method in class net.sf.basedb.core.data.LongParameterValueData

toString() - Method in class net.sf.basedb.core.data.MappingCoordinate

Get the coordinate as [plate, row, column]

toString() - Method in class net.sf.basedb.core.data.PlateCoordinate

Get the coordinate as [row, column]

toString() - Method in class net.sf.basedb.core.data.QuotaIndex

toString() - Method in class net.sf.basedb.core.data.ReporterListScoreData

toString() - Method in class net.sf.basedb.core.data.StringParameterValueData

toString() - Method in class net.sf.basedb.core.data.TextParameterValueData

toString() - Method in class net.sf.basedb.core.data.TimestampParameterValueData

toString() - Method in class net.sf.basedb.core.data.VersionedParameter

Convert the value to a string.

toString() - Method in class net.sf.basedb.core.DateParameterType

toString() - Method in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo

toString() - Method in class net.sf.basedb.core.dbengine.TableInfo.ForeignKeyInfo

toString() - Method in class net.sf.basedb.core.dbengine.TableInfo.IndexInfo

toString() - Method in class net.sf.basedb.core.dbengine.TableInfo.PrimaryKeyInfo

toString() - Method in class net.sf.basedb.core.DoubleParameterType

toString() - Method in class net.sf.basedb.core.DynamicJoin

toString() - Method in class net.sf.basedb.core.DynamicRestriction

toString() - Method in class net.sf.basedb.core.ExtraValueExpression

toString() - Method in class net.sf.basedb.core.ExtraValueJoin

toString() - Method in class net.sf.basedb.core.FeatureCoordinate

Get the coordinate as [block, row, column] or [metarow, metacolumn, row, column]

toString() - Method in enum class net.sf.basedb.core.FeatureIdentificationMethod

toString() - Method in class net.sf.basedb.core.FileParameterType

toString() - Method in class net.sf.basedb.core.FloatParameterType

toString() - Method in enum class net.sf.basedb.core.Formula.AverageMethod

toString() - Method in enum class net.sf.basedb.core.Formula.Parser

toString() - Method in enum class net.sf.basedb.core.Formula.Type

toString() - Method in class net.sf.basedb.core.IntegerParameterType

toString() - Method in enum class net.sf.basedb.core.IntensityTransform

toString() - Method in enum class net.sf.basedb.core.Item

toString() - Method in enum class net.sf.basedb.core.ItemContext.SortDirection

toString() - Method in class net.sf.basedb.core.ItemParameterType

toString() - Method in class net.sf.basedb.core.ItemProxy

toString() - Method in enum class net.sf.basedb.core.Job.ExecutionTime

toString() - Method in enum class net.sf.basedb.core.Job.Status

toString() - Method in enum class net.sf.basedb.core.Job.Type

toString() - Method in enum class net.sf.basedb.core.Location

toString() - Method in class net.sf.basedb.core.LongParameterType

toString() - Method in class net.sf.basedb.core.MeanRawDataPropertyExpression

toString() - Method in class net.sf.basedb.core.Metadata.BasicData2ItemPropertyPath

toString() - Method in class net.sf.basedb.core.Metadata.BasicItem2DataPropertyPath

toString() - Method in class net.sf.basedb.core.Metadata.CollectionPropertyPath

toString() - Method in class net.sf.basedb.core.Metadata.CombinedPropertyPath

toString() - Method in class net.sf.basedb.core.Metadata.ComponentPropertyPath

toString() - Method in class net.sf.basedb.core.Metadata.DateCopyPropertyPath

toString() - Method in class net.sf.basedb.core.Metadata.EntityPropertyPath

toString() - Method in class net.sf.basedb.core.Metadata.EvictPropertyPath

toString() - Method in class net.sf.basedb.core.Metadata.IdentifierPropertyPath

toString() - Method in class net.sf.basedb.core.Metadata.MapPropertyPath

toString() - Method in class net.sf.basedb.core.Metadata.NoopPropertyPath

toString() - Method in class net.sf.basedb.core.Metadata.ReporterScore2DataPropertyPath

toString() - Method in class net.sf.basedb.core.Metadata

toString() - Method in class net.sf.basedb.core.MigrateRbaToDba.Rba

toString() - Method in enum class net.sf.basedb.core.Operator

toString() - Method in class net.sf.basedb.core.PasswordParameterType

toString() - Method in class net.sf.basedb.core.Path

Get the string representation of the path.

toString() - Method in class net.sf.basedb.core.PathParameterType

toString() - Method in enum class net.sf.basedb.core.Permission

toString() - Method in class net.sf.basedb.core.plugin.GuiContext

toString() - Method in class net.sf.basedb.core.plugin.Permissions

toString() - Method in enum class net.sf.basedb.core.plugin.Plugin.MainType

toString() - Method in class net.sf.basedb.core.PluginParameter

toString() - Method in class net.sf.basedb.core.ProjectSpecificAnnotationsManager.AnnotationInfo

toString() - Method in class net.sf.basedb.core.PropertyFilter

toString() - Method in class net.sf.basedb.core.query.AbsExpression

toString() - Method in class net.sf.basedb.core.query.AddExpression

toString() - Method in class net.sf.basedb.core.query.AndRestriction

toString() - Method in class net.sf.basedb.core.query.AnnotationJoin

toString() - Method in class net.sf.basedb.core.query.AnyToAnyRestriction

toString() - Method in class net.sf.basedb.core.query.AscOrder

toString() - Method in class net.sf.basedb.core.query.BetweenRestriction

toString() - Method in class net.sf.basedb.core.query.BooleanExpression

toString() - Method in class net.sf.basedb.core.query.CaseExpression

toString() - Method in class net.sf.basedb.core.query.ConditionalQueryElement

toString() - Method in class net.sf.basedb.core.query.CountExpression

toString() - Method in class net.sf.basedb.core.query.DescOrder

toString() - Method in class net.sf.basedb.core.query.DivideExpression

toString() - Method in class net.sf.basedb.core.query.EqRestriction

toString() - Method in class net.sf.basedb.core.query.ExpExpression

toString() - Method in class net.sf.basedb.core.query.ExpressionSelect

toString() - Method in class net.sf.basedb.core.query.FloatExpression

toString() - Method in class net.sf.basedb.core.query.GeometricMeanExpression

toString() - Method in class net.sf.basedb.core.query.GteqRestriction

toString() - Method in class net.sf.basedb.core.query.GtRestriction

toString() - Method in class net.sf.basedb.core.query.HqlElementsExpression

toString() - Method in class net.sf.basedb.core.query.HqlEntityExpression

toString() - Method in class net.sf.basedb.core.query.HqlEntityParameterExpression

toString() - Method in class net.sf.basedb.core.query.HqlExpression

Returns the expression field.

toString() - Method in class net.sf.basedb.core.query.HqlIndexExpression

toString() - Method in class net.sf.basedb.core.query.HqlInnerJoin

toString() - Method in class net.sf.basedb.core.query.HqlLeftJoin

toString() - Method in class net.sf.basedb.core.query.HqlPropertyExpression

toString() - Method in class net.sf.basedb.core.query.HqlRightJoin

toString() - Method in class net.sf.basedb.core.query.HqlSizeExpression

toString() - Method in class net.sf.basedb.core.query.IdListRestriction

toString() - Method in class net.sf.basedb.core.query.InRestriction

toString() - Method in class net.sf.basedb.core.query.IntegerExpression

toString() - Method in class net.sf.basedb.core.query.LikeRestriction

toString() - Method in class net.sf.basedb.core.query.LogExpression

toString() - Method in class net.sf.basedb.core.query.LteqRestriction

toString() - Method in class net.sf.basedb.core.query.LtRestriction

toString() - Method in class net.sf.basedb.core.query.MaxExpression

toString() - Method in class net.sf.basedb.core.query.MeanExpression

toString() - Method in class net.sf.basedb.core.query.MinExpression

toString() - Method in class net.sf.basedb.core.query.MultiplyExpression

toString() - Method in class net.sf.basedb.core.query.NegateExpression

toString() - Method in class net.sf.basedb.core.query.NeqRestriction

toString() - Method in class net.sf.basedb.core.query.NotRestriction

toString() - Method in class net.sf.basedb.core.query.OrRestriction

toString() - Method in class net.sf.basedb.core.query.ParameterExpression

toString() - Method in class net.sf.basedb.core.query.PowerExpression

toString() - Method in class net.sf.basedb.core.query.QuadraticMeanExpression

toString() - Method in class net.sf.basedb.core.query.QueryParameter

toString() - Method in class net.sf.basedb.core.query.ReporterListExpression

toString() - Method in class net.sf.basedb.core.query.RlikeRestriction

toString() - Method in class net.sf.basedb.core.query.SelectedExpression

toString() - Method in class net.sf.basedb.core.query.SharedToRestriction

toString() - Method in class net.sf.basedb.core.query.SqlColumnExpression

toString() - Method in class net.sf.basedb.core.query.SqrtExpression

toString() - Method in class net.sf.basedb.core.query.SubqueryExpression

toString() - Method in class net.sf.basedb.core.query.SubtractExpression

toString() - Method in class net.sf.basedb.core.query.SumExpression

toString() - Method in class net.sf.basedb.core.query.ToDateExpression

toString() - Method in class net.sf.basedb.core.query.VirtualColumnExpression

toString() - Method in class net.sf.basedb.core.query.WhenStatement

toString() - Method in class net.sf.basedb.core.RawBioAssayPropertyExpression

toString() - Method in class net.sf.basedb.core.RawDataPropertyExpression

toString() - Method in class net.sf.basedb.core.RawDataType

toString() - Method in class net.sf.basedb.core.RealJoin

toString() - Method in class net.sf.basedb.core.ReporterListJoin

toString() - Method in class net.sf.basedb.core.ReporterPropertyExpression

toString() - Method in class net.sf.basedb.core.SessionControl.MainContext

toString() - Method in class net.sf.basedb.core.SessionControl.SettingInfo

toString() - Method in class net.sf.basedb.core.signal.Signal

toString() - Method in class net.sf.basedb.core.signal.SimpleSignalSender

toString() - Method in class net.sf.basedb.core.StringParameterType

toString() - Method in class net.sf.basedb.core.TimestampParameterType

toString() - Method in enum class net.sf.basedb.core.Type

toString() - Method in enum class net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType

toString() - Method in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter

toString() - Method in class net.sf.basedb.plugins.batchimport.AnnotationIdMethod

toString() - Method in class net.sf.basedb.plugins.batchimport.FallbackIdMethod

toString() - Method in class net.sf.basedb.plugins.batchimport.FileImporter.PathIdMethod

toString() - Method in class net.sf.basedb.plugins.batchimport.InternalIdMethod

toString() - Method in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod

toString() - Method in class net.sf.basedb.plugins.batchimport.PropertyIdMethod

toString() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock

toString() - Method in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper

toString() - Method in class net.sf.basedb.util.AnnotationUtil.Cache

toString() - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics

toString() - Method in class net.sf.basedb.util.bfs.EventType

toString() - Method in class net.sf.basedb.util.collections.MultiStepCollectionTransformer

toString() - Method in class net.sf.basedb.util.export.spotdata.AnnotationAssayField

toString() - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField

toString() - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField

toString() - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField

toString() - Method in class net.sf.basedb.util.extensions.events.EventType

toString() - Method in class net.sf.basedb.util.extensions.ExtensionBean

toString() - Method in class net.sf.basedb.util.extensions.ExtensionPointBean

toString() - Method in class net.sf.basedb.util.extensions.logging.LogEntry

toString() - Method in class net.sf.basedb.util.extensions.manager.ExtensionKey

toString() - Method in class net.sf.basedb.util.extensions.manager.ExtensionPointKey

toString() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile

toString() - Method in class net.sf.basedb.util.extensions.manager.FactoryParametersKey

toString() - Method in class net.sf.basedb.util.extensions.manager.PluginInfoKey

toString() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension

toString() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint

toString() - Method in class net.sf.basedb.util.extensions.xml.ExtensionPointFilter

toString() - Method in class net.sf.basedb.util.GeoLocation

toString() - Method in class net.sf.basedb.util.gtf.GtfInputStream.Attribute

toString() - Method in class net.sf.basedb.util.JarClassLoader

toString() - Method in class net.sf.basedb.util.jobagent.JobAgentInfo

Convert the information to a string that is suitable for sening as an answer to a JobAgentConnection object.

toString() - Method in class net.sf.basedb.util.jobagent.JobInfo

Convert the information to a string that is suitable for sening as an answer to a JobAgentConnection object.

toString() - Method in class net.sf.basedb.util.listable.TransformCache.CacheKey

toString() - Method in class net.sf.basedb.util.overview.Failure

toString() - Method in class net.sf.basedb.util.overview.Fix

toString() - Method in class net.sf.basedb.util.overview.loader.AutoChildNodeLoader

toString() - Method in class net.sf.basedb.util.overview.loader.ExtensionChildNodeLoader

toString() - Method in class net.sf.basedb.util.overview.Node

toString() - Method in enum class net.sf.basedb.util.overview.Severity

toString() - Method in class net.sf.basedb.util.overview.validator.ExtensionNodeValidator

toString() - Method in class net.sf.basedb.util.parser.ColumnMapper

toString() - Method in class net.sf.basedb.util.parser.CompoundMapper

toString() - Method in class net.sf.basedb.util.parser.ConstantMapper

toString() - Method in class net.sf.basedb.util.parser.FlatFileParser.Data

toString() - Method in class net.sf.basedb.util.parser.FlatFileParser.Line

toString() - Method in enum class net.sf.basedb.util.parser.FlatFileParser.LineType

toString() - Method in class net.sf.basedb.util.parser.JepMapper

toString() - Method in class net.sf.basedb.util.resources.ResourceBundleWrapper

toString() - Method in class net.sf.basedb.util.StaticCache.LockEntry

toString() - Method in class net.sf.basedb.util.StaticCache.LockSafeInputStream

toString() - Method in class net.sf.basedb.util.StaticCache.LockSafeOutputStream

toString() - Method in class net.sf.basedb.util.timer.PerformanceTimer

Print out time information about each timer.

ToStringComparator<T> - Class in net.sf.basedb.util

An implementation of the Comparator interface which uses the result of the toString method to compare the objects.

ToStringComparator(boolean) - Constructor for class net.sf.basedb.util.ToStringComparator

Create a new comparator.

toStringFormatter - Static variable in class net.sf.basedb.clients.web.taglib.table.CellValue

ToStringFormatter<T> - Class in net.sf.basedb.util.formatter

A generic formatter that simply formats objects by calling the toString() method.

ToStringFormatter() - Constructor for class net.sf.basedb.util.formatter.ToStringFormatter

Create a new integer formatter.

toStrings(Collection<T>, Formatter<T>) - Static method in class net.sf.basedb.util.Values

Convert a collection of objects to an array of strings.

total - Variable in class net.sf.basedb.core.SimpleAbsoluteProgressReporter

TOTAL - Static variable in class net.sf.basedb.core.QuotaType

The ID for the total quota.

totalBytes - Variable in class net.sf.basedb.clients.web.fileupload.FileUploadProgress

totalBytes - Variable in class net.sf.basedb.core.File.UploadStream

Number of bytes written to the stream.

totalBytes - Variable in class net.sf.basedb.plugins.PackedFileExporter

totalBytes - Variable in class net.sf.basedb.util.importer.spotdata.BfsImporter.ProgressEventHandler

totalBytes - Variable in class net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser

totalBytes - Variable in class net.sf.basedb.util.importer.spotdata.SectionReporterListParser

totalCount - Variable in class net.sf.basedb.core.AbstractResultList

totalCount - Variable in class net.sf.basedb.core.BasicBatcher

totalCount - Variable in class net.sf.basedb.core.DataResultIterator

The total number of items.

totalCount - Variable in class net.sf.basedb.core.DynamicResultIterator

The total number of items.

totalCount - Variable in class net.sf.basedb.core.ItemResultIterator

The total number of items.

totalCount - Variable in class net.sf.basedb.core.ReporterScoreResultIterator

The total number of items.

totalCount - Variable in class net.sf.basedb.core.UnmodifiableResultList

totalFileSize - Variable in class net.sf.basedb.plugins.AbstractFlatFileImporter

totalFileSize - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

totalInsertCount - Variable in class net.sf.basedb.core.FilterBatcher

The total number of inserts done by this batcher.

totalInsertCount - Variable in class net.sf.basedb.core.MappingBatcher

The total number of inserts done by this batcher.

totalInsertCount - Variable in class net.sf.basedb.core.PositionBatcher

The total number of inserts done by this batcher.

totalInsertCount - Variable in class net.sf.basedb.core.PositionExtraValueBatcher

The total number of inserts done by this batcher.

totalInsertCount - Variable in class net.sf.basedb.core.SpotBatcher

The total number of inserts done by this batcher.

totalInsertCount - Variable in class net.sf.basedb.core.SpotExtraValueBatcher

The total number of inserts done by this batcher.

totalMemory - Variable in class net.sf.basedb.util.jobagent.JobAgentInfo

totalRows - Variable in class net.sf.basedb.clients.web.taglib.table.Navigator

The total number of rows.

toType - Variable in class net.sf.basedb.core.AnyToAny.FastLinkLoader

toType - Variable in class net.sf.basedb.core.data.AnyToAnyData

toUnit(double, Unit) - Method in class net.sf.basedb.core.Unit

Convert a value from this unit to another unit.

toURLString(String) - Method in class net.sf.basedb.core.Path

Get this Path's URL-string encoded with a given character encoding.

toXml() - Method in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter

toXml(Document) - Static method in class net.sf.basedb.util.XmlUtil2

Convert a Document to xml.

toXmlFragment(boolean) - Method in class net.sf.basedb.plugins.executor.ParameterDefinition

Render this parameter definition as an XML fragment.

trace(String) - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLogger

Log a TRACE message with the related SLF4J logger.

trace(String, Throwable) - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLogger

Log a TRACE message with an optional stacktrace.

TRACE - Enum constant in enum class net.sf.basedb.util.extensions.logging.LogLevel

TRACE - Enum constant in enum class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory.Level

tracker - Variable in class net.sf.basedb.plugins.gtf.GtfReporterImporter

Needed for progress reporting since reading from the source will produce less bytes when wrapped.

tracker - Variable in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter

Needed for progress reporting since reading from the source will produce less bytes when wrapped.

tracker - Variable in class net.sf.basedb.util.parser.FlatFileParser

For keeping track of the number of bytes parsed.

Transactional - Interface in net.sf.basedb.core

This interface is a tagging interface for items that wants to be notified before a transaction is committed or after it has been completed or rollbacked.

Transactional.Action - Enum Class in net.sf.basedb.core

Enumeration constants used to tell the item what is going on in the core.

TransactionalAction - Interface in net.sf.basedb.core

Interface that define hooks for callbacks during transaction commit and rollback.

transactionalActions - Variable in class net.sf.basedb.core.DbControl

List of actions that should be performed when the transaction commits or rollbacks.

transactionDetails - Variable in class net.sf.basedb.core.LogControl

TransactionDetails - Class in net.sf.basedb.core.log

Holds information about the curren transaction, such as the logged in user, the active project, the plug-in that is executing, etc.

TransactionDetails(LogControl, SessionControl) - Constructor for class net.sf.basedb.core.log.TransactionDetails

Creates a new transaction details object with information from given session control

TransactionInfo(ChangeHistoryData) - Constructor for class net.sf.basedb.core.ChangeHistory.TransactionInfo

transactionPerFile - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

TRANSCRIPT_ID - Static variable in class net.sf.basedb.util.gtf.GtfInputStream.Attribute

transcriptIdIndex - Variable in class net.sf.basedb.util.gtf.GtfInputStream

transcriptIds - Variable in class net.sf.basedb.util.gtf.GtfInputStream

transferIsComplete() - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress

Checks if the transfer is complete or not.

transferRate - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload

The maximum transefer rate (bytes/second)

TransferRateProgressReporter - Class in net.sf.basedb.util

A progress reporter implementation that has a "side-effect" that limits the transfer rate.

TransferRateProgressReporter(AbsoluteProgressReporter, int) - Constructor for class net.sf.basedb.util.TransferRateProgressReporter

Create a new progress reporter.

TransferRateProgressReporter(AbsoluteProgressReporter, int, int) - Constructor for class net.sf.basedb.util.TransferRateProgressReporter

Create a new progress reporter.

transferredBytes - Variable in class net.sf.basedb.clients.web.fileupload.FileUploadProgress

transform - Variable in class net.sf.basedb.core.DynamicQuery

transform - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileImporter

transform - Variable in class net.sf.basedb.util.jep.ChannelFunction

transform - Variable in class net.sf.basedb.util.listable.SourceItemTransformerWithCache.TransformerWithCache

transform - Variable in class net.sf.basedb.util.listable.TransformCache.CacheKey

transform(double) - Method in enum class net.sf.basedb.core.IntensityTransform

Transform a "normal" intensity value to the transformed value.

transform(Collection<? extends I>, Collection<? super I>) - Method in class net.sf.basedb.util.collections.AddAllTransformer

Add all elements of the source collection to the destination collection.

transform(Collection<? extends I>, Collection<? super I>) - Method in class net.sf.basedb.util.collections.RemoveAllTransformer

Remove all elements in the source collection from the destination collection.

transform(Collection<? extends BasicItem>, Collection<? super Integer>) - Method in class net.sf.basedb.util.collections.BasicItemToIdTransformer

Put the ID of each BasicItem in the source collection into the destination collection.

transform(Collection<? extends S>, Collection<? super D>) - Method in interface net.sf.basedb.util.collections.CollectionTransformer

Transform the source collection and store the changes in the destination collection.

transform(Collection<? extends S>, Collection<? super D>) - Method in class net.sf.basedb.util.collections.MultiStepCollectionTransformer

Transform the source collection into the destination collection by applying all intermediate transformers specified in the constructor.

transform(DbControl, F) - Method in interface net.sf.basedb.util.transform.Transformer

Transform the given object into another object.

transform(DbControl, BioMaterialEventSourceData) - Method in class net.sf.basedb.core.BioMaterialEventSource.BioMaterialEventSourceTransformer

transform(Expression) - Method in enum class net.sf.basedb.core.IntensityTransform

Transform an expression representing a "normal" intensity value so that it represents the transformed intensity value.

transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.BioSourceToSampleTransformer

Load the ID of all samples that are immediate children to the given set of biosources.

transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.CollectedExtractsToDerivedBioAssayTransformer

transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.CollectedExtractsToRawBioAssayTransformer

transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.CollectExtracts.CollectChildren

transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.CollectExtracts.CollectFromDerivedBioAssays

transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.CollectExtracts.CollectFromExtracts

transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.CollectExtracts.CollectFromRawBioAssays

transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.CollectExtracts.CollectParents

transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.CollectExtracts.ResetCollected

transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.DerivedBioAssayToChildDerivedBioAssayTransformer

transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.DerivedBioAssayToParentDerivedBioAssayTransformer

transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.DerivedBioAssayToPhysicalBioAssayTransformer

transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.DerivedBioAssayToRawBioAssayTransformer

transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.ExtractToChildExtractTransformer

transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.ExtractToParentExtractTransformer

transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.ExtractToPhysicalBioAssayTransformer

transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.ExtractToSampleTransformer

Load the ID of all samples that are immediate parents to the given set of extracts.

transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.PhysicalBioAssayToDerivedBioAssayTransformer

transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.PhysicalBioAssayToExtractTransformer

transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.PushToParentsTransformer

transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.RawBioAssayToDerivedBioAssayTransformer

transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.RestrictionTransformer

transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.SampleToBioSourceTransformer

Load the ID of all biosources that are immediate parents to the given set of samples.

transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.SampleToChildSampleTransformer

transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.SampleToExtractTransformer

Load the ID of all extracts that are immediate children to the given set of samples.

transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.SampleToParentSampleTransformer

transform(TransformContext, Set<Integer>) - Method in interface net.sf.basedb.util.listable.SourceItemTransformer

Transform the given set of source item ID:s into a set of target item ID:s

transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.SourceItemTransformerChain

Transform the source items into target items by invoking each step in the transformer chain.

transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.SourceItemTransformerWithCache.TransformerWithCache

If a cache exists check if it has data for this transform already.

TRANSFORM_ORDER - Static variable in class net.sf.basedb.core.SyncFilter

transformation - Variable in class net.sf.basedb.core.data.BioAssaySetData

transformation - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileImporter

transformation - Variable in class net.sf.basedb.util.importer.spotdata.BfsImporter

transformation - Variable in class net.sf.basedb.util.importer.spotdata.SectionReporterListParser

Transformation - Class in net.sf.basedb.core

A transformation represents an analysis step for an Experiment.

Transformation(TransformationData) - Constructor for class net.sf.basedb.core.Transformation

Creates a new experiment item from the given data.

TRANSFORMATION - Enum constant in enum class net.sf.basedb.core.Item

The item is a Transformation

TRANSFORMATION_NAME - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

The name of the parameter that asks for the name of the transformation.

TRANSFORMATION_NAME - Static variable in class net.sf.basedb.plugins.util.Parameters

The name of the parameter that asks created by Parameters.transformationNameParameter(String, String, String)

TransformationData - Class in net.sf.basedb.core.data

This class holds information about a transformation.

TransformationData() - Constructor for class net.sf.basedb.core.data.TransformationData

transformationNameParameter(String, String, String) - Static method in class net.sf.basedb.plugins.util.Parameters

Create a plugin parameter that asks for the name of the transformation.

transformations - Variable in class net.sf.basedb.core.data.BioAssaySetData

transformations - Variable in class net.sf.basedb.core.data.ExperimentData

transformations - Variable in class net.sf.basedb.core.data.JobData

transformations - Variable in class net.sf.basedb.core.data.RawBioAssayData

TransformCache - Class in net.sf.basedb.util.listable

A simple cache implementation for holding the result of source item to target item transformation.

TransformCache(int) - Constructor for class net.sf.basedb.util.listable.TransformCache

Creates a new cache with the specified timeout.

TransformCache.CacheEntry - Class in net.sf.basedb.util.listable

TransformCache.CacheKey - Class in net.sf.basedb.util.listable

transformContext - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper

transformContext - Variable in class net.sf.basedb.core.PropertyFilter

TransformContext - Class in net.sf.basedb.util.listable

Transformation context that can be used to keep track of vital information when doing multi-step transformations.

TransformContext(DbControl) - Constructor for class net.sf.basedb.util.listable.TransformContext

Creates a new transformation context that will use the given DbControl for database access.

transformer - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn

transformer - Variable in class net.sf.basedb.core.SpecialQuery

transformer - Variable in class net.sf.basedb.util.listable.RestrictionTransformer

transformer - Variable in class net.sf.basedb.util.listable.SourceItemTransformerWithCache.TransformerWithCache

Transformer<T,F> - Interface in net.sf.basedb.util.transform

TransformerWithCache(SourceItemTransformer, SyncFilter.SourceItemTransform, String) - Constructor for class net.sf.basedb.util.listable.SourceItemTransformerWithCache.TransformerWithCache

translatePermissionsToString(Set<Permission>, String) - Static method in class net.sf.basedb.clients.web.PermissionUtil

transporter - Variable in class net.sf.basedb.core.Job.JobSignalTransporter

Trashcan - Class in net.sf.basedb.core

This class contains functionality to manage items that have been marked for deletion.

Trashcan() - Constructor for class net.sf.basedb.core.Trashcan

Trashcan.CircularRefInfo - Class in net.sf.basedb.core

Helper class for holding information about a single item, other items using it and other information that is relevant for resolving circular references.

tray - Variable in class net.sf.basedb.core.data.BioPlateData

trayColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter

trayMapper - Variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter

tree - Variable in class net.sf.basedb.util.Tree.Entry

Tree<E> - Class in net.sf.basedb.util

Tree(E) - Constructor for class net.sf.basedb.util.Tree

Create a new tree with the with the default initial capacity (16).

Tree(E, int) - Constructor for class net.sf.basedb.util.Tree

Create a new tree with the with the specified initial capacity.

Tree.ElementIterator - Class in net.sf.basedb.util

An iterator that return elements for each node.

Tree.Entry<E> - Class in net.sf.basedb.util

Represents an entry for a node in the tree.

Tree.EntryIterator - Class in net.sf.basedb.util

An iterator that return entries for each node.

trim(String, int) - Static method in class net.sf.basedb.util.Values

Trim a string to a maximum length.

trimQuotes - Variable in class net.sf.basedb.util.parser.FlatFileParser

If quotes should be trimmed from data values or not.

trimQuotes(String[]) - Method in class net.sf.basedb.util.parser.FlatFileParser

Remove enclosing quotes (" or ') around all columns.

trimQuotesParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter

Parameter definition that asks if quotes around quoted values should be removed or not.

trimString(String, int) - Static method in class net.sf.basedb.core.StringUtil

Trim a string to a maximum length.

trimString(String, int) - Static method in class net.sf.basedb.util.Values

Trims long strings to a maximum of maxLength characters.

trimStringMiddle(String, int) - Static method in class net.sf.basedb.core.StringUtil

Trim a string to a maximum length.

trimWhiteSpace - Variable in class net.sf.basedb.util.parser.FlatFileParser.Data

trimWhiteSpace - Variable in class net.sf.basedb.util.parser.FlatFileParser

If white space should be trimmed from data values or not.

TRUE - Static variable in class net.sf.basedb.core.migrate.BooleanWriter

TRUE - Static variable in class net.sf.basedb.util.excel.ExcelValue

TRUE_FALSE - Enum constant in enum class net.sf.basedb.util.formatter.BooleanFormatter.Type

Display true/false.

TRUE_FALSE_CAPS - Enum constant in enum class net.sf.basedb.util.formatter.BooleanFormatter.Type

Display TRUE/FALSE

trueValue - Variable in enum class net.sf.basedb.util.formatter.BooleanFormatter.Type

truncate(Date) - Static method in class net.sf.basedb.core.DateUtil

Truncate the given date so that only the date part remains.

trusted - Variable in class net.sf.basedb.core.data.JobAgentSettingsData

trusted - Variable in class net.sf.basedb.core.data.PluginDefinitionData

tryGetDirectoryPath - Variable in class net.sf.basedb.clients.web.taglib.Select

type - Variable in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext

type - Variable in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

type - Variable in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean

type - Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

type - Variable in class net.sf.basedb.clients.web.taglib.Input

The type of input.

type - Variable in class net.sf.basedb.clients.web.taglib.menu.Menu

If it is a vertical or horizontal menu.

type - Variable in class net.sf.basedb.clients.web.taglib.Page

The type of the current page.

type - Variable in class net.sf.basedb.core.data.FormulaData

type - Variable in class net.sf.basedb.core.data.JobData

type - Variable in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo

type - Variable in class net.sf.basedb.core.ExtendedProperty

type - Variable in class net.sf.basedb.core.FastAnnotationLoader

type - Variable in class net.sf.basedb.core.ItemProxy

type - Variable in class net.sf.basedb.core.Path

The type of the path.

type - Variable in class net.sf.basedb.core.plugin.GuiContext

type - Variable in class net.sf.basedb.core.PluginParameter

Information of the parameter type.

type - Variable in class net.sf.basedb.core.query.QueryParameter

type - Variable in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter

type - Variable in class net.sf.basedb.plugins.executor.ParameterDefinition

type - Variable in class net.sf.basedb.util.export.spotdata.AssayPropertyField

type - Variable in class net.sf.basedb.util.export.spotdata.JepDynamicField

type - Variable in class net.sf.basedb.util.export.spotdata.SimpleDynamicField

type - Variable in class net.sf.basedb.util.extensions.debug.StringConverter

type - Variable in class net.sf.basedb.util.extensions.events.EventTypeFilter

type - Variable in class net.sf.basedb.util.extensions.xml.PluginInfo

type - Variable in class net.sf.basedb.util.formatter.BooleanFormatter

type - Variable in class net.sf.basedb.util.overview.Node

type - Variable in class net.sf.basedb.util.parser.FlatFileParser.Line

type() - Method in class net.sf.basedb.util.parser.FlatFileParser.Line

The type of the line as determined by the FlatFileParser.parseHeaders() method.

Type - Enum Class in net.sf.basedb.core

This class defines constants for supported value types in BASE.

Type() - Constructor for enum class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext.Type

Type() - Constructor for enum class net.sf.basedb.core.Path.Type

Type() - Constructor for enum class net.sf.basedb.util.overview.Node.Type

Type(int) - Constructor for enum class net.sf.basedb.core.plugin.GuiContext.Type

Type(int, String) - Constructor for enum class net.sf.basedb.core.BioMaterialEvent.Type

Type(int, String) - Constructor for enum class net.sf.basedb.core.Job.Type

Type(int, String, boolean, boolean, Type) - Constructor for enum class net.sf.basedb.core.Formula.Type

Type(String, String) - Constructor for enum class net.sf.basedb.util.formatter.BooleanFormatter.Type

Type(TypeWrapper<?>, int, Class<?>, String, String, String, boolean, boolean, boolean, boolean) - Constructor for enum class net.sf.basedb.core.Type

TYPE - Static variable in class net.sf.basedb.core.Annotation

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.AnnotationSet

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.AnnotationType

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.AnnotationTypeCategory

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.AnyToAny

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.ArrayBatch

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.ArrayDesign

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.ArrayDesignBlock

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.ArrayDesignPlate

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.ArraySlide

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.BioAssay

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.BioAssaySet

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.BioMaterialEvent

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.BioPlate

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.BioPlateEvent

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.BioPlateEventParticipant

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.BioPlateEventType

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.BioPlateType

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.BioSource

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.BioWell

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.ChangeHistory

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.Client

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.ClientDefaultSetting

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.DataCube

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.DataCubeColumn

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.DataCubeExtraValue

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.DataCubeFilter

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.DataCubeLayer

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.DataFileType

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.DerivedBioAssay

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.Directory

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.DiskUsage

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.Experiment

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.Extract

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.ExtraValue

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.ExtraValueType

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.File

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.FileServer

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.FileSet

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.FileSetMember

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.Formula

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.GlobalDefaultSetting

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.Group

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.Hardware

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.Help

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.ItemKey

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.ItemList

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.ItemSubtype

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.ItemSubtypeFileType

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.Job

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.JobAgent

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.JobAgentSettings

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.Kit

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.Message

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.MimeType

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.News

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.PermissionTemplate

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.PhysicalBioAssay

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.Plate

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.PlateEvent

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.PlateEventType

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.PlateGeometry

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.PlateMapping

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.PlateType

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.Platform

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.PlatformFileType

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.PlatformVariant

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.PluginConfiguration

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.PluginDefinition

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.PluginType

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.Project

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.ProjectKey

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.Protocol

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.Quantity

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.Quota

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.QuotaType

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.RawBioAssay

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.ReporterCloneTemplate

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.ReporterList

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.ReporterType

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.Role

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.RoleKey

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.RootRawBioAssay

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.Sample

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.Session

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.Setting

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.Software

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.SyncFilter

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.Tag

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.Transformation

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.Unit

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.User

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.UserClientSetting

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.UserDefaultSetting

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.UserDevice

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.VirtualDb

The type of item represented by this class.

TYPE - Static variable in class net.sf.basedb.core.Well

The type of item represented by this class.

typeFromLength(Integer) - Static method in class net.sf.basedb.core.StringParameterType

types - Variable in class net.sf.basedb.core.log.EntityDetails

typeWrapper - Variable in enum class net.sf.basedb.core.Type

typeWrapper - Variable in class net.sf.basedb.core.VirtualColumn

The data type of the column.

TypeWrapper<T extends Type> - Class in net.sf.basedb.core.hibernate

Wrapper class for Hibernate types that will try to "hide" issues with the redesign of the type system in Hibernate that is going on in Hibernate 3.5.2 --> Hibernate 3.6.

TypeWrapper(T, int) - Constructor for class net.sf.basedb.core.hibernate.TypeWrapper

U

UMinusConverter - Class in net.sf.basedb.util.jep.convert

Convert UMinus function to a Query API Expression.

UMinusConverter() - Constructor for class net.sf.basedb.util.jep.convert.UMinusConverter

UNCONFIGURED - Enum constant in enum class net.sf.basedb.core.Job.Status

The job hasn't been configured yet.

UNDEFINED - Static variable in class net.sf.basedb.core.Quota

Quota is is not defined.

UninstalledFileProcessor - Class in net.sf.basedb.clients.web.extensions

File processor implementation that finalizes the uninstallation of an extensions file by removing it from the settings.

UninstalledFileProcessor(ProcessResults) - Constructor for class net.sf.basedb.clients.web.extensions.UninstalledFileProcessor

UninstallFilter - Class in net.sf.basedb.clients.web.extensions

Filter implementation that selects only those extensions that was selected for uninstallation by the user in the gui.

UninstallFilter(HttpServletRequest) - Constructor for class net.sf.basedb.clients.web.extensions.UninstallFilter

union(Collection<ItemList>, ItemList.DelayedAdditionManager) - Static method in class net.sf.basedb.core.ItemList

Create a set with the union of the items in the given lists.

union(Collection<ReporterList>) - Static method in class net.sf.basedb.core.ReporterList

Create a set with the union of the reporter ID:s in the given lists.

union(IdListRestriction) - Method in class net.sf.basedb.core.query.IdListRestriction

Merge this id list with another list.

unique - Variable in class net.sf.basedb.core.VirtualColumn

If the column must contain unique values or not.

unique - Variable in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod

unique - Variable in class net.sf.basedb.plugins.batchimport.PropertyIdMethod

UNIQUE - Static variable in class net.sf.basedb.core.VirtualColumn

Used in constructor to tell that the column must contain only unique values.

uniqueKeys - Variable in class net.sf.basedb.util.bfs.MetadataWriter

uniqueRandom() - Method in class net.sf.basedb.core.DbControl

Generate a random string value that is unique for the given transaction.

uniqueRandoms - Variable in class net.sf.basedb.core.DbControl

Holds random strings that must be unique within a transaction.

uniqueResult() - Method in class net.sf.basedb.core.hibernate.QueryWrapper

uniqueResultOptional() - Method in class net.sf.basedb.core.hibernate.QueryWrapper

unit - Variable in class net.sf.basedb.clients.web.plugins.ExportedProperty

unit - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef

unit - Variable in class net.sf.basedb.core.data.AnnotationData

unit - Variable in class net.sf.basedb.core.data.PropertyFilterData

unit - Variable in class net.sf.basedb.core.data.UnitSymbolData

unit - Variable in class net.sf.basedb.core.PropertyFilter

unit - Variable in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil

unit - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter.AnnotationValue

Unit - Class in net.sf.basedb.core

This class is used to represent a specific unit that can be used with annotations.

Unit(UnitData) - Constructor for class net.sf.basedb.core.Unit

Creates a unit item.

UNIT - Enum constant in enum class net.sf.basedb.core.Item

The item is a Unit.

unitCache - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter

UnitCache - Class in net.sf.basedb.util.units

Helper class for optimized lookup of units by symbol.

UnitCache() - Constructor for class net.sf.basedb.util.units.UnitCache

Create a new unit cache.

UnitCache(DbControl) - Constructor for class net.sf.basedb.util.units.UnitCache

Create a new unit cache which is ready to be used immediately.

UnitCache.CacheKey - Class in net.sf.basedb.util.units

Units are cached by (quantity,symbol) combination.

UnitConverter - Interface in net.sf.basedb.util.units

Interface for converting values between two units.

unitConvertes - Variable in class net.sf.basedb.core.AnnotationBatcher

UnitData - Class in net.sf.basedb.core.data

This class holds information units.

UnitData() - Constructor for class net.sf.basedb.core.data.UnitData

unitId - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo

unitId - Variable in class net.sf.basedb.core.FastAnnotationLoader.FastAnnotation

The ID of the unit that has been selected for this annotation.

unitId - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot

unitQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

units - Variable in class net.sf.basedb.core.data.QuantityData

units - Variable in class net.sf.basedb.util.units.UnitCache

unitSymbol - Variable in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil

UnitSymbolData - Class in net.sf.basedb.core.data

This class holds information the symbol that are used with units.

UnitSymbolData() - Constructor for class net.sf.basedb.core.data.UnitSymbolData

UnitUtil - Class in net.sf.basedb.util.units

A utility class for working with Unit:s.

UnitUtil() - Constructor for class net.sf.basedb.util.units.UnitUtil

UNKNOWN - Enum constant in enum class net.sf.basedb.util.parser.FlatFileParser.LineType

The parsed line is of an unknown type.

UnknownFunction(String) - Constructor for class net.sf.basedb.util.jep.FunctionSafeJep.UnknownFunction

unknownLines - Variable in class net.sf.basedb.util.parser.FlatFileParser

Number of unknown lines in the FlatFileParser.nextData() method.

UnknownLoginException - Exception in net.sf.basedb.core.authentication

This exception can be thrown when the login is unknown to the authentication server.

UnknownLoginException(String) - Constructor for exception net.sf.basedb.core.authentication.UnknownLoginException

Create a new UnknownLoginException object

UnknownLoginException(String, String) - Constructor for exception net.sf.basedb.core.authentication.UnknownLoginException

Create a new UnknownLoginException object

UNLIMITED - Static variable in class net.sf.basedb.core.Quota

Quota is unlimited.

unlinkAllFrom(DbControl, BasicItem) - Static method in class net.sf.basedb.core.AnyToAny

Delete all links linking from the specified item.

unlinkFrom(DbControl, BasicItem, String) - Static method in class net.sf.basedb.core.AnyToAny

unlinkJobs() - Method in class net.sf.basedb.core.Experiment

Unlink jobs from this experiment that are references from other items NOT PART of the experiment.

unload() - Static method in class net.sf.basedb.core.BatchUtil

Unload all settings.

unload() - Static method in class net.sf.basedb.core.Config

Unload all settings.

unload() - Static method in class net.sf.basedb.core.ExtendedProperties

Unload all settings.

unload() - Static method in class net.sf.basedb.core.HibernateUtil

Unload all settings.

unload() - Static method in class net.sf.basedb.core.Keyring

Unload all settings.

unload() - Static method in class net.sf.basedb.core.Metadata

Unload all settings.

unload() - Static method in class net.sf.basedb.core.PredefinedQuery

Unload all settings.

unload() - Static method in class net.sf.basedb.core.QueryExecutor

unload() - Static method in class net.sf.basedb.core.QueryRuntimeFilterFactory

Unload all settings.

unload() - Static method in class net.sf.basedb.core.RawDataTypes

Unload all settings.

unload() - Static method in class net.sf.basedb.core.RawDataUtil

Unload all settings.

unload() - Static method in class net.sf.basedb.core.SystemItems

Unload all settings.

unload() - Static method in class net.sf.basedb.util.EmailUtil

Unload all settings.

UNLOCKED - Enum constant in enum class net.sf.basedb.core.BioWell.LockMode

The well is not locked.

UnmodifiableResultList<T> - Class in net.sf.basedb.core

UnmodifiableResultList(List<T>, long) - Constructor for class net.sf.basedb.core.UnmodifiableResultList

unpack(DbControl, Directory, InputStream, File, boolean, AbsoluteProgressReporter) - Method in class net.sf.basedb.plugins.Bzip2FileUnpacker

unpack(DbControl, Directory, InputStream, File, boolean, AbsoluteProgressReporter) - Method in class net.sf.basedb.plugins.GzipFileUnpacker

unpack(DbControl, Directory, InputStream, File, boolean, AbsoluteProgressReporter) - Method in class net.sf.basedb.plugins.TarFileUnpacker

unpack(DbControl, Directory, InputStream, File, boolean, AbsoluteProgressReporter) - Method in class net.sf.basedb.plugins.ZipFileUnpacker

Use the ZipUnpacker to unpack the file.

unpack(DbControl, Directory, InputStream, File, boolean, AbsoluteProgressReporter) - Method in interface net.sf.basedb.util.zip.FileUnpacker

Unpack the given input stream into a BASE directory.

UNPACK_DIRECTORY - Static variable in class net.sf.basedb.util.zip.AbstractFileUnpacker

The name of the parameter that asks for the directory where the unpacked files are stored.

unpackType - Static variable in class net.sf.basedb.util.zip.AbstractFileUnpacker

The parameter type for unpack directory.

unpackZipFile(Directory, ZipInputStream, File, boolean, AbsoluteProgressReporter) - Method in class net.sf.basedb.util.zip.ZipUnpacker

Unpack a zip file.

unregisterAgent() - Method in class net.sf.basedb.clients.jobagent.AgentController

unregisterAllObjects(ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager

Unregister all objects know in the file.

unregisterEventHandler(EventHandler) - Method in class net.sf.basedb.util.extensions.Registry

Unregisters an event handler.

unregisterEventHandlers(ClassLoader) - Method in class net.sf.basedb.util.extensions.Registry

Unregister all event handlers that was loaded by the given class loader.

unregisterExtension(String) - Method in class net.sf.basedb.util.extensions.Registry

Unregister an extension.

unregisterExtension(ExtensionsFile.WriteableExtensionsFile, Extension<?>, Registry) - Method in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor

Unregister the given extension including factory metadata etc.

unregisterExtension(RegisterExtensionsProcessor.FileData, Extension<?>, Registry) - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor

Unregister the given extension if it is not included in the new file data information.

unregisterExtensionPoint(String) - Method in class net.sf.basedb.util.extensions.Registry

Unregister an extension point.

unregisterExtensionPoint(ExtensionsFile.WriteableExtensionsFile, ExtensionPoint<?>, Registry) - Method in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor

Unregister the given extension point including factory metadata etc.

unregisterExtensionPoint(RegisterExtensionsProcessor.FileData, ExtensionPoint<?>, Registry) - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor

Unregister the given extension point if it is not included in the new file data information.

unregisterExtensionPoints(Registry) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader

Unregister all loaded extension points from a registry.

unregisterExtensions(Registry) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader

Unregister all loaded extensions from a registry.

UnregisterExtensionsProcessor - Class in net.sf.basedb.util.extensions.manager.processor

Extensions file processor implementation that unregisters all extension points and extensions.

UnregisterExtensionsProcessor(ProcessResults) - Constructor for class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor

Create a new processor.

unregisterFactory(ExtensionsFile.WriteableExtensionsFile, Object) - Method in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor

unregisterFactory(RegisterExtensionsProcessor.FileData, Object) - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor

unregisterFileOnlyRawDataType(RawDataType) - Static method in class net.sf.basedb.core.RawDataTypes

unregisterMetadata(ObjectKey<M>) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile

Unregister metadata about an object.

unregisterObject(ObjectKey<?>, ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager

Unregister an object.

unregisterObject(ObjectKey<O>) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile

Unregister an object that was "defined" by this extensions file.

unregisterProtocols(String...) - Method in class net.sf.basedb.clients.jobagent.handlers.MultiProtocolRequestHandler

Unregister a handler for one or more protocols.

unregisterRequestHandler(String...) - Method in class net.sf.basedb.clients.jobagent.Agent

Unregister one or more protocols.

unregisterSignalHandler(SignalHandler) - Method in class net.sf.basedb.clients.web.util.SimpleSignalProgressReporter

unregisterSignalHandler(SignalHandler) - Method in class net.sf.basedb.core.signal.AbstractSignalReceiver

Unregister a signal handler.

unregisterSignalHandler(SignalHandler) - Method in class net.sf.basedb.core.signal.DelegatingSignalHandler

Unregister a signal handler.

unregisterSignalHandler(SignalHandler) - Method in interface net.sf.basedb.core.signal.SignalReceiver

Unregister a signal handler from this receiever.

UNRESTRICTED - Static variable in class net.sf.basedb.core.Quota

The ID for the unrestricted quota, which gives users unlimited disk space.

unsafe - Static variable in class net.sf.basedb.plugins.GalExporter

UNSAFE - Static variable in class net.sf.basedb.clients.web.plugins.PlainTextTemplate

UNSAFE_INLINE_SCRIPTS_ARE_ALLOWED - Static variable in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter

unsafeResources - Static variable in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter

unsafeResourcesPolicy - Variable in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter

UnsafeScriptable - Annotation Interface in net.sf.basedb.clients.web.extensions

Annotation to be used on an Action interface to mark it as a possible candidate for generating unsafe inline javascripts.

UnsavedItemException - Exception in net.sf.basedb.core

This exception is thrown when trying to use an item that has not been saved to the database in places where this is required.

UnsavedItemException() - Constructor for exception net.sf.basedb.core.UnsavedItemException

Create a new UnsavedItemException object.

UnsavedItemException(String) - Constructor for exception net.sf.basedb.core.UnsavedItemException

Create a new UnsavedItemException object with the specified message.

UnsavedItemException(String, Throwable) - Constructor for exception net.sf.basedb.core.UnsavedItemException

Create a new UnsavedItemException object with the specified message.

UnsavedItemException(Throwable) - Constructor for exception net.sf.basedb.core.UnsavedItemException

Create a new UnsavedItemException object.

unselectedText - Variable in class net.sf.basedb.clients.web.taglib.Select

Text to display that for the "unselected" option

UnsupportedFileFormatException - Exception in net.sf.basedb.core

Thrown when an import plug-in is forced to use a file that is not of the correct format.

UnsupportedFileFormatException() - Constructor for exception net.sf.basedb.core.UnsupportedFileFormatException

Create a new UnsupportedFileFormatException object.

UnsupportedFileFormatException(String) - Constructor for exception net.sf.basedb.core.UnsupportedFileFormatException

Create a new UnsupportedFileFormatException object with the specified message.

UnsupportedFileFormatException(String, Throwable) - Constructor for exception net.sf.basedb.core.UnsupportedFileFormatException

Create a new UnsupportedFileFormatException object with the specified message.

UnsupportedFileFormatException(Throwable) - Constructor for exception net.sf.basedb.core.UnsupportedFileFormatException

Create a new UnsupportedFileFormatException object.

UnsupportedSignalException - Exception in net.sf.basedb.core.signal

This exception is thrown by signal handlers and others that doesn't support a given signal.

UnsupportedSignalException(Signal) - Constructor for exception net.sf.basedb.core.signal.UnsupportedSignalException

Create a new UnsupportedSignalException.

UnsupportedSignalException(Signal, String) - Constructor for exception net.sf.basedb.core.signal.UnsupportedSignalException

Create a new UnsupportedSignalException with a custom message.

unTransform(double) - Method in enum class net.sf.basedb.core.IntensityTransform

Un-transform a transformed intensity value back to a regular intensity value.

unTransform(Expression) - Method in enum class net.sf.basedb.core.IntensityTransform

Un-transform an expression representing a transformed intensity value so that it represents a raw intensity value.

untransformIntensities - Variable in class net.sf.basedb.core.VirtualColumn

untransformIntensities() - Method in class net.sf.basedb.core.VirtualColumn

A flag indicating if transformed intensity valus belonging to a bioassay set should be untransformed as part of a query.

unverifiedDeviceInfo - Variable in class net.sf.basedb.core.SessionControl

Temporary login information before a device is verified.

UnverifiedDeviceInfo() - Constructor for class net.sf.basedb.core.SessionControl.UnverifiedDeviceInfo

unwrap() - Method in class net.sf.basedb.util.overview.cache.DirectionalCacheKey

Get the original cache key passed to the constructor.

unwrap() - Method in class net.sf.basedb.util.overview.cache.IndexedCacheKey

Get the original cache key passed to the constructor.

unwrap(Class<T>) - Method in class net.sf.basedb.core.hibernate.QueryWrapper

unwrap(Class<T>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

unwrapIfProxy(Session, BasicData) - Static method in class net.sf.basedb.core.HibernateUtil

If the given data object is a proxy, load the real data object instead.

update(D) - Method in class net.sf.basedb.core.BasicBatcher

Update a data object.

update(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

update(Object) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

update(String, Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper

update(String, Object) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

update(FeatureData) - Method in class net.sf.basedb.core.FeatureBatcher

Always throws a PermissionDeniedException, since a feature cannot be modifed once it has been created.

update(RawData) - Method in class net.sf.basedb.core.RawDataBatcher

Always throws a PermissionDeniedException, since raw data cannot be modifed once it has been created.

update(About) - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout

Update the registered information.

update(Extension<A>, ClassLoader) - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension

Update the registered information.

update(ExtensionPoint<A>, ClassLoader) - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint

Update the registered information.

Update - Class in net.sf.basedb.core

This class contains static methods used to update items already in the database.

Update() - Constructor for class net.sf.basedb.core.Update

UPDATE - Enum constant in enum class net.sf.basedb.core.hibernate.SchemaGenerator.Mode

Updating an existing installation.

UPDATE - Enum constant in enum class net.sf.basedb.core.log.ChangeType

UPDATE - Enum constant in enum class net.sf.basedb.core.Transactional.Action

The item is an existing item which is beeing updated.

UPDATE_INTERVAL - Static variable in class net.sf.basedb.core.Job.ProgressReporterImpl

Number of miliseconds between updates to the database.

UPDATE_PERCENT - Static variable in class net.sf.basedb.core.Job.ProgressReporterImpl

Min percentage difference between updates to the database.

Update.DropColumnChange - Class in net.sf.basedb.core

Action that drops a column in a table.

Update.SchemaChange - Class in net.sf.basedb.core

Action that need to make some change to the database schem after the main transaction in Update.adjustExistingItems(ProgressReporter, int, String, String) has finished.

updateable - Variable in class net.sf.basedb.core.ExtendedProperty

updateAnnotations - Variable in class net.sf.basedb.core.AnnotationBatcher

updateAnnotations(DbControl, Annotatable, Annotatable, HttpServletRequest) - Static method in class net.sf.basedb.clients.web.Base

Update annotations on an item taking concurrent modifications into account.

updateArrayDesign(ArrayDesign, FeatureIdentificationMethod, ProgressReporter) - Method in class net.sf.basedb.core.RawBioAssay

Set the ArrayDesign this raw data uses.

UpdateBatcher(Connection, String, int...) - Constructor for class net.sf.basedb.core.AnnotationBatcher.UpdateBatcher

Prepare a new batcher for the given SQL statement.

updateCount - Variable in class net.sf.basedb.core.BasicBatcher

UPDATED - Enum constant in enum class net.sf.basedb.core.AnnotationBatcher.Change

An existing annotation was updated.

updateData(Session, BasicData) - Static method in class net.sf.basedb.core.HibernateUtil

Update an existing data object in the database.

updateDatabase(ProgressReporter, String, String) - Static method in class net.sf.basedb.core.Update

Update the database by modifying existing items to follow new requirements.

updatedBytes - Variable in class net.sf.basedb.core.Experiment

updateDiskUsage(BasicItem) - Method in class net.sf.basedb.core.DbControl

Update the disk usage information for a DiskConsumable item.

updateEntry(AnnotationBatcher.UpdateBatcher) - Method in class net.sf.basedb.core.MigrateRbaToDba.Itemlist

Update the item list entry.

updateExisting - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter

updateExistingItems - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

updateFailureCountOnNodes() - Method in class net.sf.basedb.util.overview.GenericOverview

Updates the failure count (warnings and errors) on all nodes.

updateFiles(DbControl, FileStoreEnabled, HttpServletRequest, boolean, ItemContext, int) - Static method in class net.sf.basedb.clients.web.Base

Update files that are associated with a FileStoreEnabled item.

updateFreeWells(int) - Method in class net.sf.basedb.core.data.BioPlateData

Update the number of free wells with the given difference

updateFreeWells(BioPlateData, int) - Method in class net.sf.basedb.core.MeasuredBioMaterial

updateIndexes - Variable in class net.sf.basedb.core.hibernate.DbIndexWork

updateItem(DbControl, I, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Update an item with data from the current line.

updateItem(DbControl, AnnotationType, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

updateItem(DbControl, ArrayBatch, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter

updateItem(DbControl, ArrayDesign, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter

updateItem(DbControl, ArraySlide, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.ArraySlideImporter

updateItem(DbControl, BioPlate, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.BioPlateImporter

updateItem(DbControl, BioSource, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.BioSourceImporter

updateItem(DbControl, DerivedBioAssay, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

updateItem(DbControl, Extract, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.ExtractImporter

updateItem(DbControl, File, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.FileImporter

updateItem(DbControl, Kit, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.KitImporter

updateItem(DbControl, PhysicalBioAssay, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter

updateItem(DbControl, RawBioAssay, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

updateItem(DbControl, Sample, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.SampleImporter

updateItem(DbControl, Tag, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.TagImporter

updateItemLists(Connection, Map<Integer, Integer>) - Method in class net.sf.basedb.core.MigrateRbaToDba

Update item lists with raw bioassays to item lists with derived bioassays.

updateItemSubtype(DbControl, Subtypable, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

If a mapping for item subtype has been specified or if a single subtype was selected for item identification in this job, this method is will update the subtype on the item.

updateItemTable - Variable in class net.sf.basedb.core.AnnotationBatcher

updateKeys(DbControl) - Method in class net.sf.basedb.core.MultiPermissions

Generate the new keys and update all items with the new keys.

updateKeys(DbControl, boolean) - Method in class net.sf.basedb.core.MultiPermissions

Generate the new keys and update all items with the new keys.

updateLastAccess() - Method in class net.sf.basedb.core.AbstractBatcher

Update the last access time so the session control doesn't get cleaned up.

updateLastAccess() - Method in class net.sf.basedb.core.SessionControl

Update the time this object last was accessed.

updateMode - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

updateMode - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter

updateMultiLineItem(DbControl, I, FlatFileParser.Data, int) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Update an item with data from a multi-line entry.

updateMultiLineItem(DbControl, AnnotationType, FlatFileParser.Data, int) - Method in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

updateMultiLineItem(DbControl, ArrayDesign, FlatFileParser.Data, int) - Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter

Add data files

updateMultiLineItem(DbControl, DerivedBioAssay, FlatFileParser.Data, int) - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter

Add data files

updateMultiLineItem(DbControl, Extract, FlatFileParser.Data, int) - Method in class net.sf.basedb.plugins.batchimport.ExtractImporter

If the sample is pooled, add the parent sample.

updateMultiLineItem(DbControl, PhysicalBioAssay, FlatFileParser.Data, int) - Method in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter

Add parent extracts and the used quantities

updateMultiLineItem(DbControl, RawBioAssay, FlatFileParser.Data, int) - Method in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

Add data files

updateMultiLineItem(DbControl, Sample, FlatFileParser.Data, int) - Method in class net.sf.basedb.plugins.batchimport.SampleImporter

If the sample is pooled, add the parent sample.

updateOverrideId - Variable in class net.sf.basedb.core.AnnotationBatcher

updatePermissions(DbControl, Shareable, FlatFileParser.Data, boolean) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

If a mapping for a permission template has been specified for the job, this method is automatically called.

updateProgress(Session, int, String) - Method in class net.sf.basedb.core.Job.ProgressReporterImpl

updatePropertyOrder - Variable in class net.sf.basedb.core.BasicBatcher

updateRemainingQuantity(DbControl, MeasuredBioMaterialData, Float) - Static method in class net.sf.basedb.core.MeasuredBioMaterial

Update the remaining quantity of a biomaterial.

updateSource - Variable in class net.sf.basedb.core.ReporterBatcher

A string to hold the name of the source, used to update the reporters.

updateSql - Variable in class net.sf.basedb.core.BasicBatcher

updateStatement - Variable in class net.sf.basedb.core.BasicBatcher

updateToSchemaVersion101(Session) - Static method in class net.sf.basedb.core.Update

Remove duplicate file set members.

updateToSchemaVersion102(Session) - Static method in class net.sf.basedb.core.Update

Add unique index on FileSetMembers(fileset_id,datafiletype_id,file_id)

updateToSchemaVersion110(Session, int) - Static method in class net.sf.basedb.core.Update

Move derived bioassay parent items to different tables.

updateToSchemaVersion111(Session, ProgressReporter) - Static method in class net.sf.basedb.core.Update

Remove annotation sets that have no annotation values and no inherited annotations.

updateToSchemaVersion112(Session, ProgressReporter) - Static method in class net.sf.basedb.core.Update

Ensure that parent_id and parent_type in BioMaterials table is correct when compared to BioMaterialEventSources2 table.

updateToSchemaVersion114(Session, ProgressReporter) - Static method in class net.sf.basedb.core.Update

Ensure that old log entries for annotation changes use the same text format that is used after this update.

updateToSchemaVersion120(Session) - Static method in class net.sf.basedb.core.Update

Transfer existing biomaterial lists to item lists.

updateToSchemaVersion121(Session) - Static method in class net.sf.basedb.core.Update

Remove all '0' members from item lists and decrease the size of the list with 1 where it is found.

updateToSchemaVersion122(Session) - Static method in class net.sf.basedb.core.Update

Move all entries from the "ExperimentRawBioAssays" table to "RootRawBioAssays".

updateToSchemaVersion123(Session) - Static method in class net.sf.basedb.core.Update

Convert all entries from the "InheritedAnnotationSets" table to entries in the "InheritedAnnotations" table.

updateToSchemaVersion124(Session) - Static method in class net.sf.basedb.core.Update

Inherited annotations in the "InheritedAnnotations" table must be converted to entries in the "Annotations" table with source=1 (INHERITED)

updateToSchemaVersion125(Session) - Static method in class net.sf.basedb.core.Update

Experimental factors in existing experiments are inherited to the RootRawBioAssayData items from the RawBioAssayData parents.

updateToSchemaVersion126(Session) - Static method in class net.sf.basedb.core.Update

Fix the conversion formula for Fahrenheit.

updateToSchemaVersion131(Session, ProgressReporter) - Static method in class net.sf.basedb.core.Update

Fix the old_values for date annotations in the change history.

updateToSchemaVersion132(Session, ProgressReporter) - Static method in class net.sf.basedb.core.Update

Delete annotation entries that have no values.

updateToSchemaVersion136(Session, ProgressReporter) - Static method in class net.sf.basedb.core.Update

Update the Jobs table by splitting the server value into a server+node value for all entries that contain '[..]'.

updateToSchemaVersion144(Session, int) - Static method in class net.sf.basedb.core.Update

Update the Files table by setting location=0 (offline) on all files with location=2 (secondary), remove the 'action' column and all stored contexts using the 'action' column.

updateToSchemaVersion147(Session, int) - Static method in class net.sf.basedb.core.Update

updateToSchemaVersion151(Session, int, ProgressReporter) - Static method in class net.sf.basedb.core.Update

updateToSchemaVersion154(Session, int, ProgressReporter) - Static method in class net.sf.basedb.core.Update

updateURLMetadata() - Method in class net.sf.basedb.core.File

If this is an external file, try to update the metadata.

upload(InputStream, boolean) - Method in class net.sf.basedb.core.File

Upload a physical file for this file item.

upload(InputStream, boolean, Boolean) - Method in class net.sf.basedb.core.File

Upload a physical file for this file item.

Upload - Class in net.sf.basedb.clients.web.servlet

The upload servlet is used to handle single file uploads.

Upload() - Constructor for class net.sf.basedb.clients.web.servlet.Upload

UploadAbortedException - Exception in net.sf.basedb.clients.web.fileupload

UploadAbortedException() - Constructor for exception net.sf.basedb.clients.web.fileupload.UploadAbortedException

uploadCompressed - Variable in class net.sf.basedb.core.File

If the next upload should use compression or not.

uploadCompressed() - Method in class net.sf.basedb.core.File

Return the result of auto-compress check from the last call to File.setMimeTypeAuto(String, ItemSubtype).

UploadedFile - Class in net.sf.basedb.clients.web.fileupload

Objects of this class can be used to get information about an uploaded file and save the file to a directory in the filesystem.

UploadedFile(FileUpload, String, String, String) - Constructor for class net.sf.basedb.clients.web.fileupload.UploadedFile

Create a new UploadedFile object.

uploadFiles(DbControl, Directory, File, FileFilter, boolean, ProgressReporter) - Static method in class net.sf.basedb.util.FileUtil

Upload multiple files to BASE.

UploadStatus() - Constructor for class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStatus

Create a new UploadStatus object.

uploadStream - Variable in class net.sf.basedb.core.File

A stream for uploading a physical file.

UploadStream() - Constructor for class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream

UploadStream(File, boolean, boolean, boolean, boolean) - Constructor for class net.sf.basedb.core.File.UploadStream

Create a new UploadStream and connect it to the given file.

upperLimit - Variable in class net.sf.basedb.core.DoubleParameterType

The upper limit of the parameter.

upperLimit - Variable in class net.sf.basedb.core.FloatParameterType

The upper limit of the parameter.

upperLimit - Variable in class net.sf.basedb.core.IntegerParameterType

The upper limit of the parameter.

upperLimit - Variable in class net.sf.basedb.core.LongParameterType

The upper limit of the parameter.

uri - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile

uri - Variable in class net.sf.basedb.util.uri.http.HttpConnectionManager

uri - Variable in class net.sf.basedb.util.uri.UriMetadata

UriMetadata - Class in net.sf.basedb.util.uri

Holds metadata about the data referenced by given URI.

UriMetadata(URI) - Constructor for class net.sf.basedb.util.uri.UriMetadata

Create an empty metadata object for the given URI.

url - Variable in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean

url - Variable in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory

url - Variable in class net.sf.basedb.clients.web.extensions.startpage.StartPageBean

url - Variable in class net.sf.basedb.core.authentication.ExtraUserInformation

url - Variable in class net.sf.basedb.core.data.FileData

url - Variable in class net.sf.basedb.core.data.PluginDefinitionData

url - Variable in class net.sf.basedb.core.data.UserData

url - Variable in class net.sf.basedb.core.ExtendedPropertyLinker

url - Variable in class net.sf.basedb.core.plugin.AboutImpl

url - Variable in class net.sf.basedb.util.extensions.AboutBean

url - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredAbout

URL_REGEXP - Static variable in class net.sf.basedb.clients.web.util.HTML

This pattern can be used to find URL:s.

urlColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.FileImporter

urlEncode(String) - Static method in class net.sf.basedb.clients.web.util.HTML

Encode URL-unsafe characters in a string.

urlMapper - Variable in class net.sf.basedb.plugins.batchimport.FileImporter

UsableDataFileType - Interface in net.sf.basedb.core

Utility interface for collecting information about data file requirements when used on a certain platform/variant or item subtype.

UsableParentFilter() - Constructor for class net.sf.basedb.util.annotations.InheritAnnotationsManager.UsableParentFilter

usableUnitColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

Column mapping parameter for "Usable unit".

usableUnitMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

usableUnits - Variable in class net.sf.basedb.core.data.AnnotationTypeData

USE - Enum constant in enum class net.sf.basedb.core.Permission

This permission allows a user to use/link to an item.

useAutoDetection() - Method in interface net.sf.basedb.util.uri.ConnectionManagerFactory

Does this factory support auto-detection if an URI is supported or not?

useAutoDetection() - Method in class net.sf.basedb.util.uri.http.HttpConnectionManagerFactory

useBase2ColumnNames(int) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter

Reconfigure the parser to use BASE 2 column names instead of BASE 1 column names.

useBulletList() - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil

When displaying annotations with multiple values, should use a bullet list be used or a simple comma-separated list.

useCloned - Variable in class net.sf.basedb.core.ReporterPropertyExpression

useCloned(ClonableReporterQuery) - Method in class net.sf.basedb.core.ReporterPropertyExpression

Check if this reporter property should use the cloned reporter for the given query or not.

useClonedReporters - Variable in class net.sf.basedb.core.DynamicQuery

useClonedReporters - Variable in class net.sf.basedb.core.DynamicReporterQuery

useClonedReporters() - Method in interface net.sf.basedb.core.ClonableReporterQuery

Checks if this query is using cloned reporter or not by default.

useClonedReporters() - Method in class net.sf.basedb.core.DynamicQuery

Checks if this query is using cloned reporter or not by default.

useClonedReporters() - Method in class net.sf.basedb.core.DynamicReporterQuery

Checks if this query is using cloned reporter or not by default.

useCollectedAsSource - Variable in class net.sf.basedb.util.listable.CollectExtracts.CollectChildren

useCollectedAsSource - Variable in class net.sf.basedb.util.listable.CollectExtracts.CollectParents

useColors - Variable in class net.sf.basedb.core.data.ColoringData

usedColumnsParameter - Variable in class net.sf.basedb.plugins.Base1PluginExecuter

The reporter fields that should be exported as a tab separated string of column headers.

useDeviceVerification - Variable in class net.sf.basedb.core.data.UserData

usedFeatures - Variable in class net.sf.basedb.core.RawDataBatcher

Keep track of the used features to make sure that no more than raw data spot references the same feature.

usedFieldsParameter - Variable in class net.sf.basedb.plugins.Base1PluginExecuter

The spot fields that should be exported as a tab separated string of column headers.

usedFiles - Variable in class net.sf.basedb.util.bfs.AbstractDataWriterFactory

usedIds - Variable in class net.sf.basedb.util.bfs.AnnotationParser

usedIds - Variable in class net.sf.basedb.util.bfs.AnnotationWriter

useDifference() - Method in interface net.sf.basedb.core.DiskConsumable

If this item reports the difference in used bytes or the absolute number.

useDifference() - Method in class net.sf.basedb.core.Experiment

TRUE if the experiment has been saved to the database, FALSE otherwise.

useDifference() - Method in class net.sf.basedb.core.File

Always FALSE.

useDifference() - Method in class net.sf.basedb.core.RawBioAssay

Always FALSE.

usedKeys - Variable in class net.sf.basedb.util.bfs.MetadataWriter

usedMemory - Variable in class net.sf.basedb.util.jobagent.JobAgentInfo

usedQuantity - Variable in class net.sf.basedb.core.data.BioMaterialEventData

usedQuantity - Variable in class net.sf.basedb.core.data.BioMaterialEventSourceData

usedQuantity - Variable in class net.sf.basedb.core.MeasuredBioMaterial.RemainingQuantityAction

usedQuantityColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.SampleImporter

Column mapping parameter for the used quantity from the parent.

usedQuantityMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter

usedQuantityMapper - Variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter

usedQuantityMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter

UsedQuantityMapper - Class in net.sf.basedb.plugins.batchimport

A special mapper for "Used quantity" values.

UsedQuantityMapper(Mapper) - Constructor for class net.sf.basedb.plugins.batchimport.UsedQuantityMapper

usedSections - Variable in class net.sf.basedb.util.bfs.MetadataWriter

usedSlots - Variable in class net.sf.basedb.clients.jobagent.slotmanager.InternalSlotManager

usedSlots - Variable in class net.sf.basedb.core.InternalJobQueue

The current number of threads executing in each slot.

usedUnits - Variable in class net.sf.basedb.core.data.UnitData

useEditExtensions(JspContext) - Static method in class net.sf.basedb.clients.web.extensions.edit.EditUtil

Use edit-dialog extensions for a given gui context.

useExtensions(String, JspContext) - Static method in class net.sf.basedb.clients.web.extensions.edit.EditUtil

useExtensions(JspContext) - Static method in class net.sf.basedb.clients.web.extensions.list.ListColumnUtil

useExtensions(JspContext) - Static method in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil

Use toolbar extensions for a given gui context.

useExtensions(JspContext, String...) - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

Use extensions from one or more extension points.

useExtensions(JspContext, ExtensionsFilter) - Static method in class net.sf.basedb.clients.web.extensions.list.ListColumnUtil

Use list column extensions for a given gui context.

useExtensions(JspContext, ExtensionsFilter, String...) - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl

useExtensions(ClientContext, ExtensionsFilter, String...) - Method in class net.sf.basedb.util.extensions.Registry

Use extensions from one or more extension points.

useExtensions(ExtensionsFilter) - Static method in class net.sf.basedb.core.ServicesUtil

Create an extensions invoker for the services extensions.

useIncludeSpot() - Method in interface net.sf.basedb.util.DynamicFilter

If the includeSpot method must be called for each spot or not.

useIncludeSpot() - Method in class net.sf.basedb.util.IncludeExcludeFilter

Always true.

useInDistinctCount - Variable in class net.sf.basedb.core.query.ExpressionSelect

useInDistinctCount() - Method in class net.sf.basedb.core.query.ExpressionSelect

useInDistinctCount() - Method in interface net.sf.basedb.core.query.Select

If this expression should be use in count distinct queries or not.

useInternalJobQueue - Variable in class net.sf.basedb.core.data.PluginDefinitionData

useJavaSysMon - Static variable in class net.sf.basedb.clients.jobagent.handlers.InfoRequestHandler

useNewLine - Variable in class net.sf.basedb.util.ConsoleProgressReporter

useNullIfException - Variable in class net.sf.basedb.util.parser.FlatFileParser

If null should be returned if a (numeric) value can't be parsed.

useNullIfReporterNotFound - Variable in class net.sf.basedb.core.RawDataBatcher

If we should use the null reporter if a reporter isn't found.

useNullIfReporterNotFound(boolean) - Method in class net.sf.basedb.core.RawDataBatcher

Specify if the insert method should use a null reporter if a reporter with the given external ID isn't found.

useNullLoader - Variable in class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory

useNullLoaderIfNotFound() - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory

Get the null loader setting.

useNullValidator - Variable in class net.sf.basedb.util.overview.validator.BasicItemNodeValidatorFactory

useNullValidatorIfNotFound() - Method in class net.sf.basedb.util.overview.validator.BasicItemNodeValidatorFactory

Get the null validator setting.

useOnSaveExtensions(JspContext) - Static method in class net.sf.basedb.clients.web.extensions.edit.EditUtil

Use on-save extensions for a given gui context.

usePathInfo - Variable in class net.sf.basedb.clients.web.servlet.Download

usePermissions - Variable in class net.sf.basedb.core.data.PluginDefinitionData

usePluginPermissions - Variable in class net.sf.basedb.core.Keyring

If the running plugin should use specific permissions or not.

usePrefixForNull - Variable in class net.sf.basedb.util.formatter.PrefixSuffixFormatter

useProjectAnnotations - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo

user - Variable in class net.sf.basedb.core.data.BioMaterialEventData

user - Variable in class net.sf.basedb.core.data.ChangeHistoryData

user - Variable in class net.sf.basedb.core.data.ContextData

user - Variable in class net.sf.basedb.core.data.DiskUsageData

user - Variable in class net.sf.basedb.core.data.PasswordData

user - Variable in class net.sf.basedb.core.data.PlateEventData

user - Variable in class net.sf.basedb.core.data.SessionData

user - Variable in class net.sf.basedb.core.data.UserClientSettingData

user - Variable in class net.sf.basedb.core.data.UserDefaultSettingData

user - Variable in class net.sf.basedb.core.data.UserDeviceData

User - Class in net.sf.basedb.core

This class is used to represent a user in BASE.

User(UserData) - Constructor for class net.sf.basedb.core.User

USER - Enum constant in enum class net.sf.basedb.core.Item

The item is a User.

USER - Static variable in class net.sf.basedb.core.Role

The id for the Role item representing regular users.

USER_RUNTIME_FILTER - Static variable in class net.sf.basedb.core.UserClientSetting

This filter will only return items if the logged in user has generic read permission to users.

User.QueryRuntimeFilterImpl - Class in net.sf.basedb.core

A runtime filter implementation that limits a query to only return users which are members of at least one group where the logged in user is also a member unless the logged in user has generic read permission.

userAgent - Variable in class net.sf.basedb.core.data.UserDeviceData

userAgentAnalyzer - Static variable in class net.sf.basedb.util.HttpUtil

USERCLIENT_RUNTIME_FILTER - Static variable in class net.sf.basedb.core.UserClientSetting

This filter will only return items if the logged in user has generic read permission to users and clients.

UserClientSetting - Class in net.sf.basedb.core

This class is used to represent a setting valid for a specific user using a specific client application.

UserClientSetting(UserClientSettingData) - Constructor for class net.sf.basedb.core.UserClientSetting

USERCLIENTSETTING - Enum constant in enum class net.sf.basedb.core.Item

The item is an UserClientSetting.

UserClientSettingData - Class in net.sf.basedb.core.data

UserClientSettingData() - Constructor for class net.sf.basedb.core.data.UserClientSettingData

userClientSettings - Variable in class net.sf.basedb.core.SessionControl.LoginInfo

Stores name and value from UserClientSettingData.

UserData - Class in net.sf.basedb.core.data

This class holds information about a user.

UserData() - Constructor for class net.sf.basedb.core.data.UserData

UserDefaultSetting - Class in net.sf.basedb.core

This class is used to represent a setting valid for a specific user using any client application.

UserDefaultSetting(UserDefaultSettingData) - Constructor for class net.sf.basedb.core.UserDefaultSetting

USERDEFAULTSETTING - Enum constant in enum class net.sf.basedb.core.Item

The item is an UserDefaultSetting.

UserDefaultSettingData - Class in net.sf.basedb.core.data

UserDefaultSettingData() - Constructor for class net.sf.basedb.core.data.UserDefaultSettingData

userDefaultSettings - Variable in class net.sf.basedb.core.SessionControl.LoginInfo

Stores name and value from UserDefaultSettingData.

UserDevice - Class in net.sf.basedb.core

A user device represents a verified device a user may use for accessing BASE.

UserDevice(UserDeviceData) - Constructor for class net.sf.basedb.core.UserDevice

USERDEVICE - Enum constant in enum class net.sf.basedb.core.Item

The item is an UserDevice.

UserDevice.QueryRuntimeFilterImpl - Class in net.sf.basedb.core

A runtime filter implementation that limits a query to only return devices for the currently logged in user unless the logged in user has generic read permission.

UserDeviceData - Class in net.sf.basedb.core.data

This class holds information about a verified user device.

UserDeviceData() - Constructor for class net.sf.basedb.core.data.UserDeviceData

userEmail - Variable in class net.sf.basedb.core.SessionControl.UnverifiedDeviceInfo

userFilesDir - Variable in class net.sf.basedb.util.extensions.manager.Settings

userFilesDirectory - Static variable in class net.sf.basedb.core.Application

The directory where uploaded files are stored.

UserGroups - Class in net.sf.basedb.core.data.keyring

Class for mapping the UserGroups table.

UserGroups() - Constructor for class net.sf.basedb.core.data.keyring.UserGroups

Create a new UserGroups object.

userId - Variable in class net.sf.basedb.core.authentication.LoginRequest

userId - Variable in class net.sf.basedb.core.data.ChangeHistoryData

userId - Variable in class net.sf.basedb.core.data.keyring.UserGroups

userId - Variable in class net.sf.basedb.core.data.keyring.UserKeys

userId - Variable in class net.sf.basedb.core.data.keyring.UserProjects

userId - Variable in class net.sf.basedb.core.data.keyring.UserRoles

userId - Variable in class net.sf.basedb.core.Keyring

The logged in user's ID.

userId - Variable in class net.sf.basedb.core.log.TransactionDetails

userId - Variable in class net.sf.basedb.core.SessionControl.LoginInfo

The id of the UserData object for the logged in user.

UserKeys - Class in net.sf.basedb.core.data.keyring

Class for mapping the UserKeys table.

UserKeys() - Constructor for class net.sf.basedb.core.data.keyring.UserKeys

Create a new UserKeys object.

userlogin - Variable in class net.sf.basedb.core.Path

The userlogin part of the path.

userLogin - Variable in class net.sf.basedb.core.SessionControl.LoginInfo

The login property of the logged in user.

username - Variable in class net.sf.basedb.core.data.FileServerData

username - Variable in class net.sf.basedb.util.uri.ConnectionParameters

userName - Variable in class net.sf.basedb.core.log.TransactionDetails

userName - Variable in class net.sf.basedb.core.SessionControl.LoginInfo

The name property of the logged in user.

userName - Variable in class net.sf.basedb.core.SessionControl.UnverifiedDeviceInfo

userPermissions - Variable in class net.sf.basedb.core.MultiPermissions

userPermissions - Variable in class net.sf.basedb.core.UserPermissions

UserPermissions - Class in net.sf.basedb.core

This class is used to specify permissions to share an item to users.

UserPermissions() - Constructor for class net.sf.basedb.core.UserPermissions

Create a new empty object.

UserPermissions(ItemKey) - Constructor for class net.sf.basedb.core.UserPermissions

Create a new object, and initialise it with the permissions from a ItemKey.

UserProjects - Class in net.sf.basedb.core.data.keyring

Class for mapping the UserProjects table.

UserProjects() - Constructor for class net.sf.basedb.core.data.keyring.UserProjects

Create a new UserProjects object.

UserRoles - Class in net.sf.basedb.core.data.keyring

Class for mapping the UserRoles table.

UserRoles() - Constructor for class net.sf.basedb.core.data.keyring.UserRoles

Create a new UserRoles object.

users - Variable in class net.sf.basedb.core.data.GroupData

users - Variable in class net.sf.basedb.core.data.ItemKeyData

users - Variable in class net.sf.basedb.core.data.ProjectData

users - Variable in class net.sf.basedb.core.data.RoleData

users - Variable in class net.sf.basedb.core.Keyring

Holds the ID of all users which are members of at least one of the groups that the logged in user is also a member of.

users - Variable in class net.sf.basedb.core.query.SharedToRestriction

userSettings - Variable in class net.sf.basedb.core.data.ClientData

useSavePointToContinueTransactionFromSqlFailure() - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine

useSavePointToContinueTransactionFromSqlFailure() - Method in interface net.sf.basedb.core.dbengine.DbEngine

If the underlying database need to create a savepoint before executing an SQL statement that results in an error in order to be able to continue using the same transaction for other SQL queries.

useSavePointToContinueTransactionFromSqlFailure() - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine

useSeparateConnections - Variable in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration

useSeparateConnections() - Method in class net.sf.basedb.core.hibernate.SessionFactoryConfiguration

Deprecated.

Should the session factory be configured to use separate connections or is piggy-backed sessions required?

useSeparateConnections() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration

Should the session factory be configured to use separate connections or is piggy-backed sessions required?

useSmartFeatureMismatchHandling - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter

usesTo - Variable in class net.sf.basedb.core.data.AnyToAnyData

useSuffixForNull - Variable in class net.sf.basedb.util.formatter.PrefixSuffixFormatter

useThetaJoin() - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine

Most databases doesn't.

useThetaJoin() - Method in interface net.sf.basedb.core.dbengine.DbEngine

If the database uses theta join or ansi join.

useThetaJoin() - Method in class net.sf.basedb.core.dbengine.MySQLEngine

Always false.

useThetaJoin() - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine

Always false.

useThetaJoin(QueryType) - Static method in class net.sf.basedb.core.HibernateUtil

Check if theta joins or ANSI joins are used by the database.

usingItems - Variable in class net.sf.basedb.core.Trashcan.CircularRefInfo

utf8 - Variable in class net.sf.basedb.clients.web.servlet.RssNewsFeed

UTF8_WITH_FALLBACK - Static variable in class net.sf.basedb.util.charset.CharsetUtil

The provider that is providing the UTF-8 with fallback characeter sets.

Utf8PropertiesResourceBundleControl - Class in net.sf.basedb.util.resources

ResourceBundle.Control implementation that open property files in UTF-8 format instead of ISO-8859-1 format.

Utf8PropertiesResourceBundleControl() - Constructor for class net.sf.basedb.util.resources.Utf8PropertiesResourceBundleControl

utf8Tester - Variable in class net.sf.basedb.core.File.UploadStream

V

valid - Variable in class net.sf.basedb.core.data.FileSetMemberData

valid - Static variable in class net.sf.basedb.core.dbengine.AbstractDbEngine

A regexp checking for invalid characters.

valid - Static variable in class net.sf.basedb.core.ExtendedProperty

A regexp checking for invalid characters.

validActions(A[]) - Method in class net.sf.basedb.util.extensions.ActionIterator

Check that the actions array is a not-null, non-empty array and contains actions of a type that is compatible with the ExtensionPoint.getActionClass() class.

ValidAndNewOrModifiedFilter - Class in net.sf.basedb.util.extensions.manager.filter

Filter implementation for extension files that allow valid and new or modified files to pass.

ValidAndNewOrModifiedFilter(boolean) - Constructor for class net.sf.basedb.util.extensions.manager.filter.ValidAndNewOrModifiedFilter

Create a new filter.

ValidAndNewOrModifiedFilter(boolean, Filter<ExtensionsFile>) - Constructor for class net.sf.basedb.util.extensions.manager.filter.ValidAndNewOrModifiedFilter

Create a new filter.

Validatable - Interface in net.sf.basedb.core

This interface is a tagging interface for items that needs case 2 validation.

validate() - Method in class net.sf.basedb.core.BasicItem

This method is called on each Validatable item before is saved to the database.

validate() - Method in class net.sf.basedb.core.Coloring

Check that all values has been specified and that minValue <= midValue >= maxValue.

validate() - Method in class net.sf.basedb.core.Formula

validate() - Method in class net.sf.basedb.core.News

Check that startDate is before newsDate is before endDate.

validate() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

Validate that all required options has been set and that other options have sensible values.

validate() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter

validate() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile

Validate the XML file with the extension definitions.

validate(D) - Method in class net.sf.basedb.core.BasicBatcher

Validate the data, since no validation is possible in set methods of the data object.

validate(Object) - Method in enum class net.sf.basedb.core.Type

Check if an object is a value of the correct type.

validate(String, Object) - Method in class net.sf.basedb.core.ParameterType

Check if a value is valid according to the settings of this parameter type.

validate(String, List<?>) - Method in class net.sf.basedb.core.ParameterType

Check if a list of values contain invalid values.

validate(List<?>) - Method in enum class net.sf.basedb.core.Type

Check if a list of values contain only objects of the correct type.

validate(FeatureData) - Method in class net.sf.basedb.core.FeatureBatcher

Validate all properties for the feature object: The data object is not null An array design block has been specfied The position number is > 0 The external id is not null or too long The feature identification is unique The data object belongs to the correct array design The reporter match the well's reporter if a well has been specified

validate(RawData) - Method in class net.sf.basedb.core.RawDataBatcher

Validate all properties for the raw data object: The data object is not null The data object belongs to the correct raw bioassay The position value is > 0 All of the extra properties using the ExtendedProperty.validateValue(Object) method

validate(ReporterData) - Method in class net.sf.basedb.core.ReporterBatcher

Validate all properties for the reporter object: The data object is not null The name or external id is not null or too long The description or symbol is not too long All of the extendable properties using the ExtendedProperty.validateValue(Object) method

validate(DbControl) - Method in class net.sf.basedb.core.FileSet

Validate the files in this file set.

validate(Formula) - Method in enum class net.sf.basedb.core.Formula.Type

validate(ValidationAction) - Method in class net.sf.basedb.util.fileset.ValidationRenderer

VALIDATE_IMMEDIATELY - Enum constant in enum class net.sf.basedb.util.fileset.Accept

The file is handled by the validator and should be validated immediately.

VALIDATE_LATER - Enum constant in enum class net.sf.basedb.util.fileset.Accept

The file is handled by the validator but should not be validated until all files in the file set has been asked for acception.

validateAndExtractMetadata() - Method in class net.sf.basedb.util.affymetrix.CdfValidationAction

validateAndExtractMetadata() - Method in class net.sf.basedb.util.affymetrix.CelValidationAction

validateAndExtractMetadata() - Method in interface net.sf.basedb.util.fileset.ValidationAction

Validate and extract metadata from the file(s) that has been added to this validator.

validateAndExtractMetadata() - Method in class net.sf.basedb.util.gtf.GtfValidationAction

validateAnnotationValue(Object) - Method in class net.sf.basedb.core.AnnotationType

Validate an annotation value assuming that the value is in the default unit.

validateAnnotationValue(Object, Unit) - Method in class net.sf.basedb.core.AnnotationType

Validate an annotation value that can be in a different unit than the default unit.

validateCelAndCdf(FusionCELData, FusionCDFData, String) - Method in class net.sf.basedb.util.affymetrix.CelValidator

Check if the loaded CEL and CDF files matches.

validateCelAndCdf(RawBioAssay, ArrayDesign, boolean) - Static method in class net.sf.basedb.util.affymetrix.AffymetrixUtil

Check if the CEL file on the raw bioassay matches the CDF file on the array design.

validateConfiguration() - Method in class net.sf.basedb.clients.jobagent.Agent

Validate that all required configuration parameters have been specified.

validatedDom - Variable in class net.sf.basedb.clients.web.extensions.ServletLoader

validatedDom - Variable in class net.sf.basedb.util.extensions.xml.XmlLoader

validateFeatures(DbControl, ArrayDesign, FeatureIdentificationMethod, boolean, ProgressReporter) - Method in class net.sf.basedb.core.RawBioAssay

Validate that the features/reporters of the raw data matches the features/reporter on the array design.

validateKey(String) - Method in class net.sf.basedb.util.StaticCache

validateMapping(DbControl) - Method in class net.sf.basedb.core.MigrateRbaToDba.SubtypeMapping

validateMapping(DbControl, List<String>) - Method in class net.sf.basedb.core.MigrateRbaToDba.LineMapping

validateRequestParameters(List<PluginParameter<?>>, Request) - Method in class net.sf.basedb.core.plugin.AbstractPlugin

Validate the parameter values in a request against a list of plugin parameter definitions.

validateValue() - Method in class net.sf.basedb.core.query.QueryParameter

Validate the parameter value using the type information if it has been provided.

validateValue(Object) - Method in class net.sf.basedb.core.ExtendedProperty

Check if an object is valid according to the specifications of this property.

validateValue(String, Boolean) - Method in class net.sf.basedb.core.BooleanParameterType

Always validate.

validateValue(String, Double) - Method in class net.sf.basedb.core.DoubleParameterType

Checks if the value is within the range given by the upper and lower limits if those are given.

validateValue(String, Float) - Method in class net.sf.basedb.core.FloatParameterType

Checks if the value is within the range given by the upper and lower limits if those are given.

validateValue(String, Integer) - Method in class net.sf.basedb.core.IntegerParameterType

Checks if the value is within the range given by the upper and lower limits if those are given.

validateValue(String, Long) - Method in class net.sf.basedb.core.LongParameterType

Checks if the value is within the range given by the upper and lower limits if those are given.

validateValue(String, String) - Method in class net.sf.basedb.core.PathParameterType

Checks if the value is a valif Path value.

validateValue(String, String) - Method in class net.sf.basedb.core.StringParameterType

Checks if the value is a String object and shorter than the maximum length.

validateValue(String, Date) - Method in class net.sf.basedb.core.DateParameterType

Always validate.

validateValue(String, Date) - Method in class net.sf.basedb.core.TimestampParameterType

Always validate.

validateValue(String, File) - Method in class net.sf.basedb.core.FileParameterType

Always validate.

validateValue(String, T) - Method in class net.sf.basedb.core.ItemParameterType

Check if the value is in the list of allowed values.

validateValue(String, T) - Method in class net.sf.basedb.core.ParameterType

Validate a value.

validateXmlFile(InputStream, String) - Method in class net.sf.basedb.clients.web.extensions.ServletLoader

Validate an XML file against the servlet definition schema.

validateXmlFile(InputStream, String) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader

Validate an XML file against the extensions definition schema.

ValidatingFileSetMember - Class in net.sf.basedb.util.fileset

This class is a proxy used for holding information about a file set member that is currently undergoing validation.

ValidatingFileSetMember(FileSetMember) - Constructor for class net.sf.basedb.util.fileset.ValidatingFileSetMember

Create a new instance for the given real member file.

ValidationAction - Interface in net.sf.basedb.util.fileset

Action for validating and metadata extraction from files in a file set.

validationError - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile

validationOptions - Variable in class net.sf.basedb.util.overview.GenericOverview

ValidationOptions - Class in net.sf.basedb.util.overview

Stores all validation options (ie. validator -- severity) combinations.

ValidationOptions() - Constructor for class net.sf.basedb.util.overview.ValidationOptions

Create a new ValidationOptions object.

ValidationOptions(Presets.Preset) - Constructor for class net.sf.basedb.util.overview.ValidationOptions

Create a new ValidationOptions object and load settings from a preset.

ValidationRenderer - Class in net.sf.basedb.util.fileset

Renderer implementation for validating the members of a file set.

ValidationRenderer(List<ValidatingFileSetMember>, List<Throwable>) - Constructor for class net.sf.basedb.util.fileset.ValidationRenderer

Create a new renderer instance.

ValidationRuleAction - Interface in net.sf.basedb.util.overview.extensions

The same as a Validator.

validator - Variable in class net.sf.basedb.util.affymetrix.CdfValidationAction

validator - Variable in class net.sf.basedb.util.affymetrix.CelValidationAction

validator - Variable in class net.sf.basedb.util.overview.node.NodeFactory

Validator - Class in net.sf.basedb.util.overview

Placeholder for a validation rule.

Validator(String, String, String, String, Severity) - Constructor for class net.sf.basedb.util.overview.Validator

Create a new validator.

Validator(String, URL) - Constructor for class net.sf.basedb.util.XmlUtil2.Validator

Create a new instance of this class.

validators - Variable in class net.sf.basedb.util.overview.validator.BasicItemNodeValidatorFactory

validKey - Static variable in class net.sf.basedb.util.StaticCache

value - Variable in class net.sf.basedb.clients.web.extensions.DynamicActionAttribute

value - Variable in class net.sf.basedb.clients.web.taglib.Input

The value of the input element.

value - Variable in class net.sf.basedb.clients.web.taglib.table.Cell

The value to display.

value - Variable in class net.sf.basedb.clients.web.taglib.table.CellValue

The value to display.

value - Variable in class net.sf.basedb.clients.web.taglib.table.Hidden

The value of the element.

value - Variable in class net.sf.basedb.core.AnnotationSimpleRestriction

value - Variable in enum class net.sf.basedb.core.BioMaterialEvent.Type

value - Variable in enum class net.sf.basedb.core.BioWell.LockMode

The integer value of this lock mode.

value - Variable in class net.sf.basedb.core.data.PropertyFilterData

value - Variable in class net.sf.basedb.core.data.SettingData

value - Variable in class net.sf.basedb.core.DynamicRestriction

value - Variable in enum class net.sf.basedb.core.ExtraValue.CoordinateType

The integer value of this coordinate type.

value - Variable in class net.sf.basedb.core.FastAnnotationLoader.FastAnnotation

The value.

value - Variable in enum class net.sf.basedb.core.FeatureIdentificationMethod

The integer value of this method.

value - Variable in enum class net.sf.basedb.core.Formula.AverageMethod

value - Variable in enum class net.sf.basedb.core.Formula.Parser

value - Variable in enum class net.sf.basedb.core.Formula.Type

value - Variable in enum class net.sf.basedb.core.Include

value - Variable in enum class net.sf.basedb.core.IntensityTransform

The integer value of this transform.

value - Variable in enum class net.sf.basedb.core.Item

value - Variable in enum class net.sf.basedb.core.ItemContext.SortDirection

The integer value of this direction.

value - Variable in enum class net.sf.basedb.core.Job.ExecutionTime

value - Variable in enum class net.sf.basedb.core.Job.Status

value - Variable in enum class net.sf.basedb.core.Job.Type

value - Variable in enum class net.sf.basedb.core.Location

The integer value of this location.

value - Variable in enum class net.sf.basedb.core.log.ChangeType

value - Variable in enum class net.sf.basedb.core.Operator

value - Variable in enum class net.sf.basedb.core.plugin.GuiContext.Type

value - Variable in enum class net.sf.basedb.core.plugin.Plugin.MainType

value - Variable in class net.sf.basedb.core.PropertyFilter

value - Variable in class net.sf.basedb.core.query.BooleanExpression

value - Variable in class net.sf.basedb.core.query.FloatExpression

value - Variable in class net.sf.basedb.core.query.IntegerExpression

value - Variable in class net.sf.basedb.core.query.QueryParameter

value - Variable in class net.sf.basedb.core.query.WhenStatement

value - Variable in class net.sf.basedb.core.SessionControl.SettingInfo

The value of the setting, null indicates removal

value - Variable in enum class net.sf.basedb.core.Type

value - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter.AnnotationValue

value - Variable in class net.sf.basedb.util.bfs.MetadataModel.SectionEntry

value - Variable in class net.sf.basedb.util.Enumeration.Entry

value - Variable in class net.sf.basedb.util.excel.ExcelValue

value - Variable in class net.sf.basedb.util.fuzzy.StringMatcher.FuzzyMatch

value - Variable in class net.sf.basedb.util.gtf.GtfInputStream.Attribute

value - Variable in class net.sf.basedb.util.overview.filter.HasAttributeFilter

value - Variable in class net.sf.basedb.util.parser.FlatFileParser.Line

value() - Element in annotation interface net.sf.basedb.core.SubtypableRelatedItems

value() - Method in class net.sf.basedb.util.parser.FlatFileParser.Line

The value of the header if the line is a header line.

value(String) - Method in class net.sf.basedb.util.formatter.PropertyFilterFormatter

value_separator - Static variable in class net.sf.basedb.core.PropertyFilter

The string/characters used as a separator in a string with more then one filter values.

VALUE_WITH_UNIT - Static variable in class net.sf.basedb.util.units.UnitUtil

Pattern for checking if a string is a numeric value with an optional unit.

valueCache - Variable in class net.sf.basedb.util.extensions.debug.ProxyActionFactory

valueClass - Variable in enum class net.sf.basedb.core.Type

ValueConverter - Interface in net.sf.basedb.util.extensions.xml

Interface for classes that wants to inspect/convert parameters from the XML file before they are passed to factory setter methods.

valueCount - Variable in class net.sf.basedb.util.bfs.MetadataWriter

valueFormatter - Variable in class net.sf.basedb.clients.web.formatter.ExtendedPropertyFormatter

valueId - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo

valueId - Variable in class net.sf.basedb.core.data.annotations.AnnotationLink

valueIds - Variable in class net.sf.basedb.core.AnnotationBatcher

valueIndex - Variable in class net.sf.basedb.util.importer.spotdata.ExtraFloatParser

valueMapping - Static variable in enum class net.sf.basedb.core.BioMaterialEvent.Type

Maps the integer that is stored in the database.

valueMapping - Static variable in enum class net.sf.basedb.core.BioWell.LockMode

Maps an integer to a lock mode.

valueMapping - Static variable in enum class net.sf.basedb.core.ExtraValue.CoordinateType

Maps the integer that is stored in the database with an fileaction.

valueMapping - Static variable in enum class net.sf.basedb.core.FeatureIdentificationMethod

Maps an integer to a location.

valueMapping - Static variable in enum class net.sf.basedb.core.Formula.AverageMethod

Maps the integer that is stored in the database.

valueMapping - Static variable in enum class net.sf.basedb.core.Formula.Parser

Maps the integer that is stored in the database.

valueMapping - Static variable in enum class net.sf.basedb.core.Formula.Type

Maps the integer that is stored in the database.

valueMapping - Static variable in enum class net.sf.basedb.core.IntensityTransform

Maps an integer to a transform.

valueMapping - Static variable in enum class net.sf.basedb.core.Item

valueMapping - Static variable in enum class net.sf.basedb.core.ItemContext.SortDirection

Maps an integer to a sort direction.

valueMapping - Static variable in enum class net.sf.basedb.core.Job.ExecutionTime

Maps the integer that is stored in the database.

valueMapping - Static variable in enum class net.sf.basedb.core.Job.Status

Maps the integer that is stored in the database.

valueMapping - Static variable in enum class net.sf.basedb.core.Job.Type

Maps the integer that is stored in the database.

valueMapping - Static variable in enum class net.sf.basedb.core.Location

Maps an integer to a location.

valueMapping - Static variable in enum class net.sf.basedb.core.Operator

valueMapping - Static variable in enum class net.sf.basedb.core.plugin.GuiContext.Type

Maps the integer that is stored in the database.

valueMapping - Static variable in enum class net.sf.basedb.core.plugin.Plugin.MainType

Maps an integer to a type.

valueMapping - Static variable in enum class net.sf.basedb.core.Type

valueOf(String) - Static method in enum class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext.Type

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.clients.web.extensions.menu.MenuItemAction.MenuType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.core.Annotation.Source

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.core.AnnotationBatcher.Change

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.core.BioMaterialEvent.Type

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.core.BioWell.LockMode

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.core.ExtraValue.CoordinateType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.core.FeatureIdentificationMethod

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.core.Formula.AverageMethod

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.core.Formula.Parser

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.core.Formula.Type

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.core.hibernate.SchemaGenerator.Mode

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.core.Include

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.core.IntensityTransform

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.core.Item

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.core.ItemContext.AddFilter

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.core.ItemContext.SortDirection

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.core.ItemList.SynchronizeOption

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.core.Job.ExecutionTime

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.core.Job.Status

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.core.Job.Type

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.core.Location

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.core.log.ChangeType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.core.Operator

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.core.Path.Type

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.core.Permission

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.core.plugin.GuiContext.Type

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.core.plugin.Plugin.MainType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.core.plugin.Response.Status

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.core.query.JoinType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.core.query.QuerySection

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.core.query.QueryType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.core.ReporterCloneBatcher.CloneSource

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.core.SyncFilter.SourceItemTransform

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.core.Transactional.Action

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.core.Type

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.core.VirtualTable

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.FormatType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.util.extensions.logging.LogLevel

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory.Level

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.util.extensions.xml.PathType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.util.fileset.Accept

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.util.formatter.BooleanFormatter.Type

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.util.overview.node.ChildNodeDirection

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.util.overview.Node.Type

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.util.overview.Severity

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.util.parser.FlatFileParser.LineType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.util.plot.HistogramPlot.YAggregate

Returns the enum constant of this class with the specified name.

values - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo

values - Variable in class net.sf.basedb.core.AnnotationInRestriction

values - Variable in class net.sf.basedb.core.AnnotationSimpleRestriction

values - Variable in class net.sf.basedb.core.data.AnnotationData

values - Variable in class net.sf.basedb.core.data.BooleanParameterValueData

values - Variable in class net.sf.basedb.core.data.DateParameterValueData

values - Variable in class net.sf.basedb.core.data.DoubleParameterValueData

values - Variable in class net.sf.basedb.core.data.FloatParameterValueData

values - Variable in class net.sf.basedb.core.data.IntegerParameterValueData

values - Variable in class net.sf.basedb.core.data.ItemParameterValueData

values - Variable in class net.sf.basedb.core.data.LongParameterValueData

values - Variable in class net.sf.basedb.core.data.StringParameterValueData

values - Variable in class net.sf.basedb.core.data.TextParameterValueData

values - Variable in class net.sf.basedb.core.data.TimestampParameterValueData

values - Variable in class net.sf.basedb.core.ParameterInfo

values - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot

values - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations

values - Variable in class net.sf.basedb.plugins.executor.ProgramParameter

values - Variable in class net.sf.basedb.util.bfs.MetadataModel.SectionEntry

values - Variable in class net.sf.basedb.util.plot.PlotAnnotation

values() - Static method in enum class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext.Type

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.clients.web.extensions.menu.MenuItemAction.MenuType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.core.Annotation.Source

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.core.AnnotationBatcher.Change

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.core.BioMaterialEvent.Type

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.core.BioWell.LockMode

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.core.ExtraValue.CoordinateType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.core.FeatureIdentificationMethod

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.core.Formula.AverageMethod

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.core.Formula.Parser

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.core.Formula.Type

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.core.hibernate.SchemaGenerator.Mode

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.core.Include

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.core.IntensityTransform

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.core.Item

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.core.ItemContext.AddFilter

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.core.ItemContext.SortDirection

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.core.ItemList.SynchronizeOption

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.core.Job.ExecutionTime

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.core.Job.Status

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.core.Job.Type

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.core.Location

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.core.log.ChangeType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.core.Operator

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.core.Path.Type

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.core.Permission

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.core.plugin.GuiContext.Type

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.core.plugin.Plugin.MainType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.core.plugin.Response.Status

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.core.query.JoinType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.core.query.QuerySection

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.core.query.QueryType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.core.ReporterCloneBatcher.CloneSource

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.core.SyncFilter.SourceItemTransform

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.core.Transactional.Action

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.core.Type

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.core.VirtualTable

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.FormatType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.util.extensions.logging.LogLevel

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory.Level

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.util.extensions.xml.PathType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.util.fileset.Accept

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.util.formatter.BooleanFormatter.Type

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.util.overview.node.ChildNodeDirection

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.util.overview.Node.Type

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.util.overview.Severity

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.util.parser.FlatFileParser.LineType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.util.plot.HistogramPlot.YAggregate

Returns an array containing the constants of this enum class, in the order they are declared.

Values - Class in net.sf.basedb.core

Utility class to handle the conversion between data objects and item objects.

Values - Class in net.sf.basedb.util

This class contains a set of static methods that may be useful for handling strings, ints and other values.

Values() - Constructor for class net.sf.basedb.core.Values

Values() - Constructor for class net.sf.basedb.util.Values

valuesPermissions - Variable in class net.sf.basedb.core.ChangeHistory

valueType - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean

valueType - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory

valueType - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef

The type of data in the property.

valueType - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo

valueType - Variable in class net.sf.basedb.core.AnnotationRestriction

valueType - Variable in class net.sf.basedb.core.data.AnnotationTypeData

valueType - Variable in class net.sf.basedb.core.data.DataCubeExtraValueData

valueType - Variable in class net.sf.basedb.core.data.ExtraValueTypeData

valueType - Variable in class net.sf.basedb.core.data.FormulaData

valueType - Variable in class net.sf.basedb.core.data.PropertyFilterData

valueType - Variable in class net.sf.basedb.core.data.ReporterClonePropertyData

valueType - Variable in enum class net.sf.basedb.core.Formula.Type

valueType - Variable in class net.sf.basedb.core.ParameterInfo

valueType - Variable in class net.sf.basedb.core.ParameterType

The matching type of parameter values (can be null)

valueType - Variable in class net.sf.basedb.core.PositionExtraValueBatcher

The type of values to insert.

valueType - Variable in class net.sf.basedb.core.PropertyFilter

valueType - Variable in class net.sf.basedb.core.query.ParameterExpression

valueType - Variable in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil

valueType - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot

valueType - Variable in class net.sf.basedb.core.SpotExtraValueBatcher

The type of values to insert.

valueType - Variable in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod

valueType - Variable in class net.sf.basedb.plugins.batchimport.PropertyIdMethod

valueTypeColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

Column mapping parameter for the annotation value type

ValueTypeFormatter - Class in net.sf.basedb.util.formatter

Formatter implementation that converts an integer into it's Type representation and the uses name() as the formatted value.

ValueTypeFormatter() - Constructor for class net.sf.basedb.util.formatter.ValueTypeFormatter

Create a new formatter.

ValueTypeFormatter(String) - Constructor for class net.sf.basedb.util.formatter.ValueTypeFormatter

Create a new formatter.

valueTypeMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter

VARIABLE - Static variable in class net.sf.basedb.util.extensions.xml.VariableConverter

variableConverter - Variable in class net.sf.basedb.clients.web.extensions.WebClientRegisterExtensionsProcessor

VariableConverter - Class in net.sf.basedb.util.extensions.xml

A value converter that can be used on all setter methods that has been annotated with the VariableSetter annotation.

VariableConverter() - Constructor for class net.sf.basedb.util.extensions.xml.VariableConverter

Create a new variable converter.

variables - Variable in class net.sf.basedb.util.extensions.xml.VariableConverter

VariableSetter - Annotation Interface in net.sf.basedb.util.extensions.xml

Indicates that a factory setter method which takes a string as it's input will have the value scanned by a VariableConverter before the setter method is invoked.

variant - Variable in class net.sf.basedb.core.data.ArrayDesignData

variant - Variable in class net.sf.basedb.core.data.FileTypeIndex

variant - Variable in class net.sf.basedb.core.data.PlatformFileTypeData

variant - Variable in class net.sf.basedb.core.data.RawBioAssayData

variant - Variable in class net.sf.basedb.core.RawDataType

variantColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter

variantColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

variantId - Variable in class net.sf.basedb.core.MigrateRbaToDba.LineMapping

variantId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba

variantMapper - Variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter

variantMapper - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

variantQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

variants - Variable in class net.sf.basedb.core.data.PlatformData

vdb - Variable in class net.sf.basedb.core.DynamicJoin

vdb - Variable in class net.sf.basedb.core.ExtraValueJoin

VELOCITY - Static variable in class net.sf.basedb.core.Quantity

The id for the Quantity object representing velocity.

verificationCode - Variable in class net.sf.basedb.core.SessionControl.UnverifiedDeviceInfo

verificationCode - Variable in class net.sf.basedb.core.User

verifiedEmail - Variable in class net.sf.basedb.core.User

verify(String, SSLSession) - Method in class net.sf.basedb.util.ssl.AllowAnyHostNameVerifyer

verifyBaseVersion(About, boolean) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader

verifyColumns - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter

verifyDevice(String, boolean) - Method in class net.sf.basedb.core.SessionControl

Call this method to verify a device.

verifyOnly - Variable in class net.sf.basedb.core.authentication.LoginRequest

verifyRootLoginAndPassword(String, String) - Static method in class net.sf.basedb.core.Update

Verify the root user login and password.

verifySchemaVersion - Variable in class net.sf.basedb.core.Application.StartupOptions

verifySchemaVersion - Variable in enum class net.sf.basedb.core.hibernate.SchemaGenerator.Mode

verifySchemaVersion() - Method in enum class net.sf.basedb.core.hibernate.SchemaGenerator.Mode

Does this installation mode require a check against the schema version of the intalled database or not?

verifySchemaVersion(boolean) - Method in class net.sf.basedb.core.Application.StartupOptions

Set to FALSE when starting a new installation or upgrade.

verifyUserExternal(Session, LoginRequest, List<AuthenticationManager>) - Method in class net.sf.basedb.core.SessionControl

Verify the user with external authentication.

verifyUserInternal(LoginRequest) - Method in class net.sf.basedb.core.AuthenticationContext

Check that the user exists and verify the password using internal authentication.

verifyUserInternal(Session, LoginRequest) - Method in class net.sf.basedb.core.SessionControl

Verify the user with internal authentication.

version - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo

version - Variable in class net.sf.basedb.core.data.BasicData

version - Variable in class net.sf.basedb.core.data.PluginDefinitionData

version - Variable in class net.sf.basedb.core.data.VersionedParameter

The version of the parameter.

version - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba

version - Variable in class net.sf.basedb.core.plugin.AboutImpl

version - Variable in class net.sf.basedb.util.extensions.AboutBean

version - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredAbout

Version - Class in net.sf.basedb.core

Get information about the BASE version.

Version() - Constructor for class net.sf.basedb.core.Version

VERSION - Static variable in class net.sf.basedb.core.ClonableProperty

The property name of the "static" property BasicData.getVersion().

VersionedParameter - Class in net.sf.basedb.core.data

The key to a plugin configuration parameter.

VersionedParameter() - Constructor for class net.sf.basedb.core.data.VersionedParameter

Used by Hibernate to create an instance.

VersionedParameter(String, int) - Constructor for class net.sf.basedb.core.data.VersionedParameter

Create a new instance.

versionNumberParameter - Variable in class net.sf.basedb.plugins.Base1PluginExecuter

The version number of the plug-in.

versionString - Variable in class net.sf.basedb.core.data.HardwareData

versionString - Variable in class net.sf.basedb.core.data.SoftwareData

vertical - Variable in class net.sf.basedb.clients.web.taglib.ButtonGroup

If the buttons should be vertically grouped.

vetoAuthenticatedUser(UserData, AuthenticatedUser) - Method in interface net.sf.basedb.core.authentication.AuthenticationManager

This method is called if there are multiple installed external authentication managers and at least one of them accepted the user in the AuthenticationManager.authenticate() method.

VIEW - Enum constant in enum class net.sf.basedb.core.log.ChangeType

ViewAndDownloadActionFactory - Class in net.sf.basedb.clients.web.extensions.fileviewer

Facotry for creating the "View" and "Download" actions in file lists.

ViewAndDownloadActionFactory() - Constructor for class net.sf.basedb.clients.web.extensions.fileviewer.ViewAndDownloadActionFactory

VIRTUAL - Enum constant in enum class net.sf.basedb.core.ReporterCloneBatcher.CloneSource

Use the position-to-reporter mapping in the experiment.

VirtualColumn - Class in net.sf.basedb.core

This class is used to define columns in the virtual tables in the dynamic part of the database that are storing analysed data.

VirtualColumn(String, String, TypeWrapper<?>, int, boolean, boolean, boolean, boolean, boolean) - Constructor for class net.sf.basedb.core.VirtualColumn

Create a new virtual column.

VirtualColumnExpression - Class in net.sf.basedb.core.query

VirtualColumnExpression(VirtualTable, VirtualColumn) - Constructor for class net.sf.basedb.core.query.VirtualColumnExpression

VirtualColumnExpression.WrappedExpression - Class in net.sf.basedb.core.query

virtualDb - Variable in class net.sf.basedb.core.data.DataCubeData

virtualDb - Variable in class net.sf.basedb.core.data.ExperimentData

virtualDb - Variable in class net.sf.basedb.core.DynamicQuery

virtualDb - Variable in class net.sf.basedb.core.DynamicReporterQuery

virtualDb - Variable in class net.sf.basedb.core.ReporterCloneBatcher

VirtualDb - Class in net.sf.basedb.core

A virtual database represents the set of tables in the dynamic database used by a single experiment to store it's analysed data.

VirtualDb(VirtualDbData) - Constructor for class net.sf.basedb.core.VirtualDb

Creates a new experiment item from the given data.

VIRTUALDB - Enum constant in enum class net.sf.basedb.core.Item

The item is a VirtualDb

VirtualDbData - Class in net.sf.basedb.core.data

This class holds information about a virtual database in the dynamic part of Base.

VirtualDbData() - Constructor for class net.sf.basedb.core.data.VirtualDbData

VirtualTable - Enum Class in net.sf.basedb.core

This enumeration defines constants that are used to specify different virtual tables in the dynamic part of the database used for analysis.

VirtualTable(String, String, VirtualColumn...) - Constructor for enum class net.sf.basedb.core.VirtualTable

Creates a new virtual table.

virtualTableExists(VirtualDb, VirtualTable) - Static method in class net.sf.basedb.core.HibernateUtil

Check if a table exists in the dynamic database or not.

visible - Variable in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory

visible - Variable in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean

visible - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory

visible - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory

visible - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean

visible - Variable in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean

visible - Variable in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory

visible - Variable in class net.sf.basedb.clients.web.taglib.Button

If the button should be visible or not.

visible - Variable in class net.sf.basedb.clients.web.taglib.Help

If the help icon should be visible or not.

visible - Variable in class net.sf.basedb.clients.web.taglib.HideableSection

If the section should be visible or not.

visible - Variable in class net.sf.basedb.clients.web.taglib.Icon

If the icon should be visible or not.

visible - Variable in class net.sf.basedb.clients.web.taglib.Input

If the input should be visible or not.

visible - Variable in class net.sf.basedb.clients.web.taglib.menu.Menuitem

If the menu item is visible.

visible - Variable in class net.sf.basedb.clients.web.taglib.menu.Menuseparator

If the separator is visible.

visible - Variable in class net.sf.basedb.clients.web.taglib.menu.Submenu

If the menu item is visible.

visible - Variable in class net.sf.basedb.clients.web.taglib.path.PathElement

visible - Variable in class net.sf.basedb.clients.web.taglib.Select

If the select list should be visible or not.

visible - Variable in class net.sf.basedb.clients.web.taglib.tab.Tab

If the tab should be visible or not.

visible - Variable in class net.sf.basedb.clients.web.taglib.table.Button

If the button should be visible or not.

visible - Variable in class net.sf.basedb.clients.web.taglib.table.Cell

If the cell should be visible or not.

visible - Variable in class net.sf.basedb.clients.web.taglib.table.Header

If the header should be visible or not.

visible - Variable in class net.sf.basedb.clients.web.taglib.table.Label

If the button should be visible or not.

visible - Variable in class net.sf.basedb.clients.web.taglib.table.Navigator

If the navigator bar should be visible or not.

visible - Variable in class net.sf.basedb.clients.web.taglib.table.Panel

If the panel should be visible or not.

visible - Variable in class net.sf.basedb.clients.web.taglib.table.PresetSelector

If the preset selector should be visible or not.

visible - Variable in class net.sf.basedb.clients.web.taglib.table.Row

If the row should be visible or not.

visible - Variable in class net.sf.basedb.clients.web.taglib.table.Toolbar

If the toolbar should be visible or not.

visible - Variable in class net.sf.basedb.clients.web.taglib.Zoom

If the zoom icon should be visible or not.

visibleColumns - Variable in class net.sf.basedb.clients.web.taglib.table.Table

The ID of all visible columns, sorted by the order they should appear.

visiblePermission - Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory

visiblePermission - Variable in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory

visibleProperties - Static variable in class net.sf.basedb.core.ExtendedProperties

A map from class name --> a list of extended properties of for that class.

vLeft - Variable in class net.sf.basedb.core.RealJoin

vLeftColumn - Variable in class net.sf.basedb.core.RealJoin

VOLUME - Static variable in class net.sf.basedb.core.Quantity

The id for the Quantity object representing volume.

W

wait - Variable in class net.sf.basedb.clients.jobagent.executors.DummyJobExecutor

WAITING - Enum constant in enum class net.sf.basedb.core.Job.Status

The job is waiting to be started.

warn(String) - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLogger

Log a WARNING message.

warn(String, String, String) - Static method in class net.sf.basedb.clients.web.taglib.DeprecationLogger

Log a warning for using the given taglib and attribute.

warn(String, Throwable) - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLogger

Log a WARNING message with an optional stacktrace.

WARN - Enum constant in enum class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory.Level

warning(SAXParseException) - Method in class net.sf.basedb.util.XmlUtil2.Validator

Ignore warnings

WARNING - Enum constant in enum class net.sf.basedb.util.extensions.logging.LogLevel

WARNING - Enum constant in enum class net.sf.basedb.util.overview.Severity

The rule generate warnings.

was - Variable in enum class net.sf.basedb.core.log.ChangeType

was(String) - Method in enum class net.sf.basedb.core.log.ChangeType

Create a string for display purposes that explains what has happened to the what.

wasModified - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile

wasModified() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile

Check if the file was modified when the last call to ExtensionsFile.checkModified() was made.

WasProcessedFilter - Class in net.sf.basedb.util.extensions.manager.filter

Filter implementation that passes all extension files that has been processed according to the information in the given ProcessResults object.

WasProcessedFilter(ProcessResults) - Constructor for class net.sf.basedb.util.extensions.manager.filter.WasProcessedFilter

WEBCLIENT_ID - Static variable in class net.sf.basedb.clients.web.Base

The external ID of the web client application.

WebClientRegisterExtensionsProcessor - Class in net.sf.basedb.clients.web.extensions

A subclass to the regular extensions processor that adds information about various paths (eg. home path, servlet path) on the web client as variables in the XmlLoader that is used to process the definition files.

WebClientRegisterExtensionsProcessor(String, String, String, ProcessResults) - Constructor for class net.sf.basedb.clients.web.extensions.WebClientRegisterExtensionsProcessor

WebException - Exception in net.sf.basedb.clients.web

This exception can be thrown on any JSP page in BASE.

WebException(String, String, String) - Constructor for exception net.sf.basedb.clients.web.WebException

Create a new WebException.

WebException(String, String, String, Object...) - Constructor for exception net.sf.basedb.clients.web.WebException

Create a new WebException.

weightedLeastSquaresRegression(List<LowessNormalization.SpotData>, List<Double>) - Static method in class net.sf.basedb.plugins.LowessNormalization

well - Variable in class net.sf.basedb.core.data.FeatureData

Well - Class in net.sf.basedb.core

A well is located on a Plate and contains a ReporterData.

Well(WellData) - Constructor for class net.sf.basedb.core.Well

WELL - Enum constant in enum class net.sf.basedb.core.Item

The item is a Well.

WellCoordinateFormatter - Class in net.sf.basedb.util.formatter

Formats an internal well coordinate to an external coordinate.

WellCoordinateFormatter(boolean) - Constructor for class net.sf.basedb.util.formatter.WellCoordinateFormatter

Create a well coordinate formatter.

WellData - Class in net.sf.basedb.core.data

This class holds information about a well on a plate.

WellData() - Constructor for class net.sf.basedb.core.data.WellData

wells - Variable in class net.sf.basedb.core.data.PlateData

what - Variable in class net.sf.basedb.util.Diff3

WhenStatement - Class in net.sf.basedb.core.query

Create a WHEN statement to be used in a CaseExpression.

WhenStatement(Restriction, Expression) - Constructor for class net.sf.basedb.core.query.WhenStatement

Create a new WhenStatement

whenStatements - Variable in class net.sf.basedb.core.query.CaseExpression

WHERE - Enum constant in enum class net.sf.basedb.core.query.QuerySection

WHICH_ITEMS - Static variable in class net.sf.basedb.clients.web.plugins.SimpleExport

WHICH_PROPERTIES - Static variable in class net.sf.basedb.clients.web.plugins.SimpleExport

width - Variable in class net.sf.basedb.clients.web.extensions.plot.MAPlotFactory

width - Variable in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean

width - Variable in class net.sf.basedb.clients.web.taglib.table.Form

width - Variable in class net.sf.basedb.core.data.AnnotationTypeData

width - Variable in class net.sf.basedb.core.ParameterType

Width of the input field for the parameter in the GUI.

withPrefix(String, String) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification

Return prefix+string if string is not null or the empty string otherwise.

work - Variable in class net.sf.basedb.core.hibernate.SavePointWork

workbook - Variable in class net.sf.basedb.clients.web.plugins.XlsxTemplate

workbook - Variable in class net.sf.basedb.util.excel.CellStyleCreator

workbook - Variable in class net.sf.basedb.util.excel.XlsxTableWriter

workbook - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil

WorkbookStream() - Constructor for class net.sf.basedb.util.excel.XlsxToCsvUtil.WorkbookStream

workDir - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor

Temporary working directory at runtime.

workerThread - Variable in class net.sf.basedb.core.signal.EnhancedThreadSignalHandler

The worker thread that should be interrupted when a signal is received.

workerThread - Variable in class net.sf.basedb.core.signal.ThreadSignalHandler

The worker thread that should be interrupted when Signal.ABORT is received.

wrap(Logger) - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLogger

Wrap a generic SLF4J logger with this logger.

wrapForReset(SourceItemTransformer) - Method in class net.sf.basedb.util.listable.CollectExtracts

Wraps the parent transformer with a ResetCollected transformer the first time this method is called.

wrapInputStream(InputStream) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter

This method is called before the parser starts reading from the input stream.

wrapInputStream(InputStream) - Method in class net.sf.basedb.plugins.gtf.GtfReporterImporter

Wrap the input stream with a GtfInputStream.

wrapInputStream(InputStream) - Method in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter

Wrap the input stream with a GtfInputStream.

wrapInputStream(InputStream) - Method in interface net.sf.basedb.util.parser.WrappedConfigureByExample

Wrap an input stream within another stream, for example, a gzip input stream.

WrappedConfigureByExample - Interface in net.sf.basedb.util.parser

This is an extension to the ConfigureByExample interface that allows a plug-in to wrap an input stream with another stream.

WrappedExpression(String) - Constructor for class net.sf.basedb.core.query.VirtualColumnExpression.WrappedExpression

WrappedFormatter<T> - Class in net.sf.basedb.util.excel

Excel formatter implementation that uses the value from any parent formatter and creates a string cell value.

WrappedFormatter(Formatter<T>) - Constructor for class net.sf.basedb.util.excel.WrappedFormatter

wrapper - Variable in class net.sf.basedb.clients.web.taglib.extensions.Render

WrappingRenderer<A extends Action> - Interface in net.sf.basedb.util.extensions

An extension to the regular renderer interface intended for renderers that wants to wrap an existing renderer to give the result their own touch.

write - Static variable in class net.sf.basedb.core.Item.DefinedPermissions

write() - Method in class net.sf.basedb.core.migrate.BooleanWriter

write() - Method in class net.sf.basedb.core.migrate.ByteArrayWriter

write() - Method in class net.sf.basedb.core.migrate.DateWriter

write() - Method in class net.sf.basedb.core.migrate.DoubleWriter

write() - Method in class net.sf.basedb.core.migrate.FloatWriter

write() - Method in class net.sf.basedb.core.migrate.IntegerWriter

write() - Method in class net.sf.basedb.core.migrate.LongWriter

write() - Method in interface net.sf.basedb.core.migrate.ResultWriter

Write the current data.

write() - Method in class net.sf.basedb.core.migrate.ShortWriter

write() - Method in class net.sf.basedb.core.migrate.TextWriter

write() - Method in class net.sf.basedb.core.migrate.TimestampWriter

write(byte[]) - Method in class net.sf.basedb.core.File.UploadStream

write(byte[]) - Method in class net.sf.basedb.core.plugin.ExportOutputStream

write(byte[], int, int) - Method in class net.sf.basedb.core.File.CharsetTesterThread

Runs in the main thread.

write(byte[], int, int) - Method in class net.sf.basedb.core.File.UploadStream

write(byte[], int, int) - Method in class net.sf.basedb.core.plugin.ExportOutputStream

write(char[]) - Method in class net.sf.basedb.util.excel.XlsxTableWriter

write(char[], int, int) - Method in class net.sf.basedb.util.excel.XlsxTableWriter

write(int) - Method in class net.sf.basedb.core.File.CharsetTesterThread

Runs in the main thread.

write(int) - Method in class net.sf.basedb.core.File.UploadStream

Writes the specified byte to this buffered output stream.

write(int) - Method in class net.sf.basedb.core.plugin.ExportOutputStream

write(int) - Method in class net.sf.basedb.util.excel.XlsxTableWriter

write(String) - Method in class net.sf.basedb.util.excel.XlsxTableWriter

write(String, int) - Method in class net.sf.basedb.util.StaticCache

Get an output stream that can be used to write binary information to the cache.

write(String, int, int) - Method in class net.sf.basedb.util.excel.XlsxTableWriter

write(String, InputStream, int) - Method in class net.sf.basedb.util.StaticCache

Store binary information in the cache.

WRITE - Enum constant in enum class net.sf.basedb.core.Permission

This permission allows a user update the information about an item.

WriteableExtensionsFile(ExtensionsFile) - Constructor for class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile

Creates a new writeable extensions file.

writeableFile - Variable in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor.FileData

writeAnnotations(ExportedProperty, List<?>, String) - Method in interface net.sf.basedb.clients.web.plugins.ExportTemplate

Write annotation values.

writeAnnotations(ExportedProperty, List<?>, String) - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate

Join the annotation values into a single string with a comma.

writeAnnotations(ExportedProperty, List<?>, String) - Method in class net.sf.basedb.clients.web.plugins.XlsxTemplate

Join the annotation values into a single string with a comma.

writeAnnotations(ExportedProperty, List<?>, String) - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate

Add annotation values to the current item element.

writeCollection(ExportedProperty, Collection<?>) - Method in interface net.sf.basedb.clients.web.plugins.ExportTemplate

Write the values in a collection

writeCollection(ExportedProperty, Collection<?>) - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate

Writes a collection of values.

writeCollection(ExportedProperty, Collection<?>) - Method in class net.sf.basedb.clients.web.plugins.XlsxTemplate

Writes a collection of values.

writeCollection(ExportedProperty, Collection<?>) - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate

Add collection values to the current item element.

writeColumnFilters(int) - Method in class net.sf.basedb.clients.web.taglib.table.Table

writeColumns() - Method in class net.sf.basedb.clients.web.taglib.table.Table

writeColumnSubtitles(StringBuilder) - Method in class net.sf.basedb.clients.web.taglib.table.Table

writeData(Object, boolean) - Method in class net.sf.basedb.util.excel.XlsxTableWriter

Write the data to the next cell.

writeDataHeader(PrintWriter) - Method in class net.sf.basedb.plugins.GalExporter

Write the data header.

writeFeature(PrintWriter, FeatureData, ArrayDesignBlock) - Method in class net.sf.basedb.plugins.GalExporter

Write feature data.

writeHeaders() - Method in interface net.sf.basedb.clients.web.plugins.ExportTemplate

Write headers.

writeHeaders() - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate

Write the headers on a single line.

writeHeaders() - Method in class net.sf.basedb.clients.web.plugins.XlsxTemplate

Write the headers on a single row.

writeHeaders() - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate

Write property and annotation definitions.

writeHeaders(PrintWriter, List<String>) - Method in class net.sf.basedb.plugins.GalExporter

Write the headers of the GAL file, including the two first lines with the "ATF 1.0" line and the second line with the number of header lines and the number of data columns.

writeLock() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile

Try to aquire a write-lock.

writeLock() - Method in class net.sf.basedb.util.StaticCache.LockEntry

writeMissingFeature(PrintWriter, FeatureCoordinate) - Method in class net.sf.basedb.plugins.GalExporter

Write a missing features.

writeObject(ObjectOutputStream) - Method in class net.sf.basedb.clients.web.taglib.extensions.Render

writeObject(ObjectOutputStream) - Method in class net.sf.basedb.clients.web.taglib.extensions.Scripts

writeObject(ObjectOutputStream) - Method in class net.sf.basedb.clients.web.taglib.extensions.Stylesheets

writeObject(ObjectOutputStream) - Method in class net.sf.basedb.clients.web.taglib.table.ExtensionCells

writeObject(ObjectOutputStream) - Method in class net.sf.basedb.core.data.ContextIndex

writeObject(ObjectOutputStream) - Method in class net.sf.basedb.core.data.FileTypeIndex

writeObject(ObjectOutputStream) - Method in class net.sf.basedb.core.data.QuotaIndex

writeObject(ObjectOutputStream) - Method in class net.sf.basedb.core.data.ReporterListScoreData

writeObject(ObjectOutputStream) - Method in class net.sf.basedb.core.log.LoggingInterceptor

writeObject(ObjectOutputStream) - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot

writeObject(ObjectOutputStream) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot

writeObject(ObjectOutputStream) - Method in class net.sf.basedb.util.jep.FunctionSafeJep.SafeFunctionTable

writePermissions - Variable in class net.sf.basedb.core.Job.SignalKeyring

writeProperty(ExportedProperty, Object) - Method in interface net.sf.basedb.clients.web.plugins.ExportTemplate

Write the specified property values.

writeProperty(ExportedProperty, Object) - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate

Write the data object.

writeProperty(ExportedProperty, Object) - Method in class net.sf.basedb.clients.web.plugins.XlsxTemplate

Write the data object.

writeProperty(ExportedProperty, Object) - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate

Add the property value to the current item element.

writeProtected - Variable in class net.sf.basedb.core.data.FileData

writeProtected - Variable in class net.sf.basedb.core.ParameterValuesImpl

The configuration should only be writeable when configuring the job, not while executing a job.

writer - Variable in class net.sf.basedb.core.migrate.AbstractResultWriter

writeTo(OutputStream) - Method in class net.sf.basedb.clients.web.fileupload.UploadedFile

Upload the file and write the data to the specified output stream.

writeTo(OutputStream) - Method in class net.sf.basedb.core.Presets

Write the prestes to a stream as an XML file.

writeTo(Cell, CellStyleCreator) - Method in class net.sf.basedb.util.excel.ExcelValue.BlankValue

writeTo(Cell, CellStyleCreator) - Method in class net.sf.basedb.util.excel.ExcelValue.BooleanValue

writeTo(Cell, CellStyleCreator) - Method in class net.sf.basedb.util.excel.ExcelValue.DateValue

writeTo(Cell, CellStyleCreator) - Method in class net.sf.basedb.util.excel.ExcelValue.IntValue

writeTo(Cell, CellStyleCreator) - Method in class net.sf.basedb.util.excel.ExcelValue.NumericValue

writeTo(Cell, CellStyleCreator) - Method in class net.sf.basedb.util.excel.ExcelValue.StringValue

writeTo(Cell, CellStyleCreator) - Method in class net.sf.basedb.util.excel.ExcelValue

Write the value to the given cell and apply a format to it with the help of the style creator.

writeTrailingColumns - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil

writeValue(Serializable, ObjectOutputStream) - Method in enum class net.sf.basedb.core.Type

Write a value of this type to the output stream.

X

x - Variable in class net.sf.basedb.core.data.RawData

x - Variable in class net.sf.basedb.util.plot.HistogramPlot.TempSeries

xColumnMapping - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

XJspCompiler - Class in net.sf.basedb.clients.web.extensions

Class that enabled compilation of custom JSP pages that are part of an extension that uses classes from the extension JAR file (eg. a JAR file in the /WEB-INF/extensions directory).

XJspCompiler() - Constructor for class net.sf.basedb.clients.web.extensions.XJspCompiler

XLSX_MIME_TYPE - Static variable in class net.sf.basedb.util.excel.XlsxToCsvUtil

The MIME type for Excel workbook files.

XlsxTableWriter - Class in net.sf.basedb.util.excel

This is a simple wrapper for the TableWriter class to make it create an Excel workbook instead of a CSV file.

XlsxTableWriter(String) - Constructor for class net.sf.basedb.util.excel.XlsxTableWriter

Create a new workbook with a single worksheet.

XlsxTableWriter(Workbook, String) - Constructor for class net.sf.basedb.util.excel.XlsxTableWriter

Add a sheet to the given Excel workbook.

XlsxTemplate - Class in net.sf.basedb.clients.web.plugins

Template implementation that exports data to Excel format (xlsx).

XlsxTemplate(OutputStream, List<ExportedProperty>, Item, long, String) - Constructor for class net.sf.basedb.clients.web.plugins.XlsxTemplate

Create a new template.

XlsxToCsvUtil - Class in net.sf.basedb.util.excel

Utility class for converting Excel worksheets to CSV-formatted InputStreams.

XlsxToCsvUtil() - Constructor for class net.sf.basedb.util.excel.XlsxToCsvUtil

Create a new instance using defult settings.

XlsxToCsvUtil.CellTypeWithInfo - Class in net.sf.basedb.util.excel

XlsxToCsvUtil.SheetInfo - Class in net.sf.basedb.util.excel

Represents a single sheet in a workbook.

XlsxToCsvUtil.WorkbookStream - Class in net.sf.basedb.util.excel

Input stream implementation that combines streams from all sheets in the current workbook.

xMapper - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

xmlFile - Variable in class net.sf.basedb.plugins.HelpImporter

xmlFile - Variable in class net.sf.basedb.plugins.PluginConfigurationImporter

xmlFileParameter - Static variable in class net.sf.basedb.plugins.PluginConfigurationImporter

XmlLoader - Class in net.sf.basedb.util.extensions.xml

Loads extension points and extensions from extension definition XML files.

XmlLoader() - Constructor for class net.sf.basedb.util.extensions.xml.XmlLoader

Create a new XML loader instance.

xmlOut - Variable in class net.sf.basedb.clients.web.plugins.XMLTemplate

xmlOut - Variable in class net.sf.basedb.util.extensions.xml.XmlLoader

xmlParserClass - Static variable in class net.sf.basedb.util.XmlUtil2

The parser class we are using.

XMLTemplate - Class in net.sf.basedb.clients.web.plugins

A XML template that exports data in a simple one-level XML format.

XMLTemplate(Writer, List<ExportedProperty>, Item) - Constructor for class net.sf.basedb.clients.web.plugins.XMLTemplate

Create a new template.

XmlUtil2 - Class in net.sf.basedb.util

This class contains some useful methods for handling XML documents using JDOM2.

XmlUtil2() - Constructor for class net.sf.basedb.util.XmlUtil2

XmlUtil2.Validator - Class in net.sf.basedb.util

This class is used to handle callbacks from the XML parser.

xtFile - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile

xtFile - Variable in class net.sf.basedb.util.extensions.manager.ProcessResults.FileResults

xtFiles - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsManager

xtId - Variable in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory.MySkinAction

xtManager - Static variable in class net.sf.basedb.core.Application

Manager for the extensions system.

xtra(Integer) - Method in class net.sf.basedb.util.jep.ExtraValueFunction

Get the value of the specified extra value of the current sql result.

xtValidators - Variable in class net.sf.basedb.util.overview.validator.ExtensionNodeValidator

xtVersions - Static variable in class net.sf.basedb.clients.web.taglib.Head

Y

y - Variable in class net.sf.basedb.core.data.RawData

y - Variable in class net.sf.basedb.util.plot.HistogramPlot.TempSeries

yAggregate - Variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramSeries

YAggregate() - Constructor for enum class net.sf.basedb.util.plot.HistogramPlot.YAggregate

yColumnMapping - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

YES_NO - Enum constant in enum class net.sf.basedb.util.formatter.BooleanFormatter.Type

Display yes/no.

yMapper - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter

ywRangeFactor - Static variable in class net.sf.basedb.plugins.LowessNormalization

Z

ZERO - Static variable in class net.sf.basedb.core.DiskUsageStatistics

ZERO_SET - Static variable in class net.sf.basedb.core.AbstractHqlQuery

ZERO_SET - Static variable in class net.sf.basedb.core.QueryRuntimeFilterFactory

zip - Variable in class net.sf.basedb.util.zip.ZipFilePacker

ZIP_FILE - Static variable in class net.sf.basedb.util.zip.AbstractFileUnpacker

The name of the parameter that asks for the file that is going to be unpacked.

ZipFilePacker - Class in net.sf.basedb.util.zip

This class packs files into a ZIP archive.

ZipFilePacker() - Constructor for class net.sf.basedb.util.zip.ZipFilePacker

Create a new packer that compresses files with the zip format.

zipFileType - Static variable in class net.sf.basedb.util.zip.AbstractFileUnpacker

The parameter type for file to unpack.

ZipFileUnpacker - Class in net.sf.basedb.plugins

A plugin for unpacking zip and jar file on the BASE file system.

ZipFileUnpacker() - Constructor for class net.sf.basedb.plugins.ZipFileUnpacker

ZipUnpacker - Class in net.sf.basedb.util.zip

This class can be used to unpack zip files into the BASE directory structure.

ZipUnpacker(DbControl) - Constructor for class net.sf.basedb.util.zip.ZipUnpacker

Create a new zip unpacker.

Zoom - Class in net.sf.basedb.clients.web.taglib

This tag is used to make it easier to add zoom features on a BASE web page.

Zoom() - Constructor for class net.sf.basedb.clients.web.taglib.Zoom

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