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

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.

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

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

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

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

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.

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

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

AbstractRPCClient - Class in net.sf.basedb.ws.client

Abstract class for RPCServiceClients in web services.

AbstractRPCClient(String, String) - Constructor for class net.sf.basedb.ws.client.AbstractRPCClient

AbstractRPCClient(String, String, ServiceFactory) - Constructor for class net.sf.basedb.ws.client.AbstractRPCClient

AbstractRPCService - Class in net.sf.basedb.ws.server

An abstract class for Web service classes to extend from.

AbstractRPCService() - Constructor for class net.sf.basedb.ws.server.AbstractRPCService

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

AbstractSqlQuery - Class in net.sf.basedb.core

An abstract implementation of the SqlQuery interface.

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

abstractText - Variable in class net.sf.basedb.info.ExperimentInfo

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

The id for the Quantity object representing acceleration.

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

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

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

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

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

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

action - Variable in class net.sf.basedb.core.data.FileData

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

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

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

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

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

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

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.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

activate - Variable in class net.sf.basedb.clients.web.taglib.tab.Tab

A JavaScript method that is invoked when activating the tab.

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

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.

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

Not supported.

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

Not supported.

add(BioMaterial) - Method in class net.sf.basedb.core.BioMaterialList

Add a biomaterial to this list.

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

Add multiple biomaterials to this list in one go.

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

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

This operation is not supported.

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

Add two expressions: new expression = e1 + e2.

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

Register a system item.

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

Not supported.

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

Not supported.

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

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

Not supported.

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

Add all items from another biomaterial list to this list.

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

Add all reporters from another reporter list to this list.

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

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.

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

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.

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

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

Add a category to this annotation type.

addChange(ChangeType, Object, Object[], Object[], String[], Type[]) - 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(Node) - Method in class net.sf.basedb.util.overview.Node

Add a child node to this one.

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

Add a child to the node.

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.

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

Add a column to a table.

addColumnDef(ColumnDef) - 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, float, HistogramPlot.YAggregate, HistogramPlot.YAggregate) - Method in class net.sf.basedb.util.plot.HistogramPlot

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.

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

Add data to the plot.

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

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.

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

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

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

Add a new entry to this section.

addEntry(String, String...) - 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.

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.

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

Store information about an uploaded file.

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

Add an entry to the 'files' section.

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

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

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

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

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

Add <filter> conditions to the given class tag.

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

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

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

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

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<BioMaterialList>) - Method in class net.sf.basedb.core.BioMaterialList

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.

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<BioMaterialData>) - Method in class net.sf.basedb.core.BioMaterialList

Add members to this list.

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.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.HybridizationImporter

Deprecated. 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.LabeledExtractImporter

Deprecated. 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.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.ScanImporter

Deprecated. Adds column mappings for name, internalId, description, hybridization, protocol, hardware, image-file, image-name, image-format and image-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.HybridizationImporter

Deprecated.

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.RawBioAssayImporter

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

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

Deprecated. Add parameter for "Image directory" directory where image 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.

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.

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

Grant permissions to a user, 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.UserPermissions

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

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

Adds a single plate to the plate list.

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(Configuration) - 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

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

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

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

The postal address to the user.

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

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.

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.

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.

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

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.

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(Configuration, 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(Configuration) - 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.

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

Add a symbol to this unit.

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

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.

addToList(BioMaterialList, Collection<? extends S>, CollectionTransformer<S, ? extends BioMaterial>) - Static method in class net.sf.basedb.util.biomaterial.ListUtil

Adds items to a biomaterial list.

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

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

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

Adds a value to the number of transfered bytes.

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

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.

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) - Method in class net.sf.basedb.core.BasicItem

Add items to the set of items using this one.

addUsingItems(Set<ItemProxy>, Query) - 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, 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.

affectedRows - Variable in class net.sf.basedb.core.hibernate.ExecuteUpdateWork

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

affiliations - Variable in class net.sf.basedb.info.ExperimentInfo

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 - 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.

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

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 net.sf.basedb.core.Item

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

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

Same as property(alias, null).

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 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_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 net.sf.basedb.core.Item

align - Variable in class net.sf.basedb.clients.web.taglib.ButtonGroup

Optional align attribute

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 enum net.sf.basedb.core.Include

A non-modifable collection containing all options.

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

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

Create a subquery expression: ANY (subquery).

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

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

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

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

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.

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

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

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

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

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

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

allowSaveParameters() - Method in enum 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

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

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.

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.

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

Update index statistics for a table.

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 ...

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.

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.

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<D extends AnnotatedData> - Class in net.sf.basedb.core

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

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

AnnotatedItemInfo - Class in net.sf.basedb.info

AnnotatedItemInfo() - Constructor for class net.sf.basedb.info.AnnotatedItemInfo

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

Create an annotation assay field.

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

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

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.

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.

AnnotationBetweenRestriction - Class in net.sf.basedb.core

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

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

Create a new annotation restriction.

AnnotationBetweenRestriction(String, int, Type, Object, Object, boolean) - 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

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.AnnotationValue(Object, Unit) - Constructor for class net.sf.basedb.plugins.AnnotationFlatFileImporter.AnnotationValue

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

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

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

Create a new cache for the specified item.

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

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

AnnotationInfo - Class in net.sf.basedb.info

An information class that holds information about annotation values for a given annotation type.

AnnotationInfo() - Constructor for class net.sf.basedb.info.AnnotationInfo

Creates information object with no properties set.

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, Object...) - Constructor for class net.sf.basedb.core.AnnotationInRestriction

Create a new annotation restriction.

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

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

Create a new annotation restriction for an annotation type.

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

Create a new annotation restriction given the id and value type of an annotation.

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 - 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

annotations - Variable in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot

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 - 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 - 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.WellData

annotationSet - Variable in class net.sf.basedb.util.overview.validator.ProtocolParameterValidator

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

AnnotationSet.QueryRuntimeFilterImpl() - Constructor for class net.sf.basedb.core.AnnotationSet.QueryRuntimeFilterImpl

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.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(boolean) - 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.

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, AnnotationType, Operator, Object, boolean) - Constructor for class net.sf.basedb.core.AnnotationSimpleRestriction

Create a new annotation restriction using a simple expression: annotation operator value.

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

Creates a new annotation restriction for a specific valueType.

AnnotationSimpleRestriction(String, int, Type, Operator, List<Object>, boolean) - 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.

annotationType - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary

annotationType - Variable in class net.sf.basedb.clients.web.plugins.ExportedProperty

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 - Variable in class net.sf.basedb.core.data.AnnotationData

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

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

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

AnnotationTypeClient - Class in net.sf.basedb.ws.client

Web service client for annotation types.

AnnotationTypeClient(SessionClient) - Constructor for class net.sf.basedb.ws.client.AnnotationTypeClient

Creates new AnnotationTypeClient object for an active session client.

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

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(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.snapshot.AnnotationSnapshot

annotationTypeId - Variable in class net.sf.basedb.core.snapshot.AnnotationTypeFilter

annotationTypeId - Variable in class net.sf.basedb.info.AnnotationInfo

annotationTypeIds - Variable in class net.sf.basedb.clients.web.ExperimentExplorer

The currently selected annotation types on the view page.

AnnotationTypeInfo - Class in net.sf.basedb.info

An information class that holds information about an AnnotationType.

AnnotationTypeInfo() - Constructor for class net.sf.basedb.info.AnnotationTypeInfo

Creates information object with no properties set.

annotationTypes - Variable in class net.sf.basedb.core.data.AnnotationTypeCategoryData

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

Section definition for grouping all mappings of columns to annotation types.

AnnotationTypeService - Class in net.sf.basedb.ws.server

Web service class for annotation types.

AnnotationTypeService() - Constructor for class net.sf.basedb.ws.server.AnnotationTypeService

AnnotationUtil - Class in net.sf.basedb.util

Utility class for working with annotations.

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 the RawBioAssay.getParentExtract() property until we have loaded the Extracts of a Physical Bioassay.

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

AnnotationValidator - Class in net.sf.basedb.util.overview.validator

Validator implementation for annotations.

AnnotationValidator() - Constructor for class net.sf.basedb.util.overview.validator.AnnotationValidator

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

Create a subquery expression: ANY (subquery).

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.

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

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

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

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 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

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 the first 8 columns to the buffer and then add all values from the attributes.

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, boolean) - 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, SessionControl, boolean) - Method in class net.sf.basedb.clients.web.taglib.Head

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.DbCleaner() - Constructor for class net.sf.basedb.core.Application.DbCleaner

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.Pinger(SessionControl) - Constructor for class net.sf.basedb.core.Application.Pinger

Application.SecondaryStorageControllerTask - Class in net.sf.basedb.core

Application.SecondaryStorageControllerTask(SecondaryStorageController) - Constructor for class net.sf.basedb.core.Application.SecondaryStorageControllerTask

Application.SessionControlCacheCleaner - Class in net.sf.basedb.core

Application.SessionControlCacheCleaner() - Constructor for class net.sf.basedb.core.Application.SessionControlCacheCleaner

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.

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.

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 - 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 - Variable in class net.sf.basedb.core.data.ArraySlideData

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 - 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 - 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

ArrayDesignBlock - Class in net.sf.basedb.core

ArrayDesignBlock(ArrayDesignBlockData) - Constructor for class net.sf.basedb.core.ArrayDesignBlock

arrayDesignBlock - Variable in class net.sf.basedb.core.data.FeatureData

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

ArrayDesignClient - Class in net.sf.basedb.ws.client

A web service client for array design in BASE.

ArrayDesignClient(SessionClient) - Constructor for class net.sf.basedb.ws.client.ArrayDesignClient

Creates a new client object for a session.

arrayDesignColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter

arrayDesignColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter

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

arrayDesignData - Variable in class net.sf.basedb.core.FeatureBatcher

Just a copy of the data object for the array design.

arrayDesignHasBeenSet - Variable in class net.sf.basedb.core.RawBioAssay

arrayDesignId - Variable in class net.sf.basedb.info.RawBioAssayInfo

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

ArrayDesignInfo - Class in net.sf.basedb.info

Information class for a ArrayDesign in BASE.

ArrayDesignInfo() - Constructor for class net.sf.basedb.info.ArrayDesignInfo

Creates a new empty info object.

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

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.PlateData

ArrayDesignService - Class in net.sf.basedb.ws.server

Web service class for ArrayDesign Provides services to access limited functionality in this class.

ArrayDesignService() - Constructor for class net.sf.basedb.ws.server.ArrayDesignService

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

arrayIndexColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.HybridizationImporter

Deprecated.

arrayIndexMapper - Variable in class net.sf.basedb.plugins.batchimport.HybridizationImporter

Deprecated.

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 - Class in net.sf.basedb.core

This class represents a physical microarray slide.

ArraySlide(ArraySlideData) - Constructor for class net.sf.basedb.core.ArraySlide

arraySlide - Variable in class net.sf.basedb.core.data.PhysicalBioAssayData

arraySlideColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.HybridizationImporter

Deprecated.

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.HybridizationImporter

Deprecated.

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

asc(Expression) - Static method in class net.sf.basedb.core.query.Orders

Sort the result of a query in ascending order by the expression.

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

asFloat - Variable in class net.sf.basedb.util.parser.ConstantMapper

asInteger - Variable in class net.sf.basedb.util.parser.ConstantMapper

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

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

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.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.

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.

attachFile(DataSource, String) - Method in class net.sf.basedb.ws.server.AbstractRPCService

Attach a file to an OMElement so it can be sent with webservices.

attribute - Variable in class net.sf.basedb.util.overview.filter.HasAttributeFilter

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

attributes - Variable in class net.sf.basedb.clients.web.taglib.Body

Any other attributes that is needed in the body tag.

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.gtf.GtfInputStream

attributes - Variable in class net.sf.basedb.util.overview.Node

authenticate(String, String) - Method in interface net.sf.basedb.core.authentication.Authenticator

Authenticates a user.

authenticate(String, String) - Method in class net.sf.basedb.core.authentication.POP3Authenticator

Authenticates a user against the POP3 server.

authenticate(String, String) - Method in class net.sf.basedb.core.authentication.SimpleAuthenticator

If login and password are equal the user is authenticated, otherwise an InvalidPasswordException is thrown.

authenticationDriver - Static variable in class net.sf.basedb.core.Application

The name of the external authenication class, if any.

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(Throwable) - 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

AuthenticationInformation - Class in net.sf.basedb.core.authentication

Objects of this class are returned by the Authenticator.authenticate(String,String) method and contains information about the authenticated user.

AuthenticationInformation(String, String) - Constructor for class net.sf.basedb.core.authentication.AuthenticationInformation

Creates a new AuthenticationInformation object without extra information.

AuthenticationInformation(String, String, String, String, String, String, String, String, String, String) - Constructor for class net.sf.basedb.core.authentication.AuthenticationInformation

Creates a new AuthenticationInformation object with extra information.

Authenticator - Interface in net.sf.basedb.core.authentication

This interface defines the methods that needs to be implemented by a class to be able to use it for external authentication against another database or directory service.

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

authors - Variable in class net.sf.basedb.info.ExperimentInfo

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

If tab height should be automatically adjusted or not.

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.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.

AutoDetectFileFormat.IsImportableFilter(File, Filter<? super ContextUtil.ContextResult>) - Constructor for class net.sf.basedb.util.AutoDetectFileFormat.IsImportableFilter

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.

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 This method will only consider parent items that the logged in user has access to with USE permission.

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

autoLoadChildren - Variable in class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory

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.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.ExtendedProperty

averageMethod - Variable in enum 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

averageOnReporter - Variable in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter

avg - Variable in class net.sf.basedb.core.query.GeometricMeanExpression

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 - 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 - Variable in class net.sf.basedb.core.query.LogExpression

base - Variable in class net.sf.basedb.core.query.PowerExpression

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.

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 in net.sf.basedb.plugins

Base1PluginExecuter.Base1JobParameterType(char) - Constructor for enum net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType

Base1PluginExecuter.JobParameter - Class in net.sf.basedb.plugins

Base1PluginExecuter.JobParameter(String...) - Constructor for class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter

Base1PluginExecuter.JobParameter(Element) - Constructor for class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter

base64_code - Static variable in class net.sf.basedb.util.bcrypt.BCrypt

BASE_VERSION - Static variable in class net.sf.basedb.clients.web.taglib.Page

The version of BASE.

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.

BaseFileDataSource - Class in net.sf.basedb.ws.server

BaseFileDataSource(File) - Constructor for class net.sf.basedb.ws.server.BaseFileDataSource

Creates a new DataSourceObject for a file.

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

BaseFileExporterPlugin.ExtendedDynamicField(String, boolean, DynamicField) - Constructor for class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField

BaseFileExporterPlugin.ExtendedDynamicField(String, String, boolean, DynamicField) - Constructor for class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField

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.RawDataProxy() - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileImporter.RawDataProxy

BaseFileImporter.ReporterProxy - Class in net.sf.basedb.util.importer.spotdata

BaseFileImporter.ReporterProxy() - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileImporter.ReporterProxy

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.ChildBioAssay() - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay

Create a new object.

BaseFileInfo.ChildBioAssay(int) - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay

Create a new object

BaseFileInfo.SpotSectionInfo - Class in net.sf.basedb.util.importer.spotdata

Keeps information about headers and more in a 'spot' section.

BaseFileInfo.SpotSectionInfo() - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo

Creates a new object.

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.

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<D extends BasicData> - Class in net.sf.basedb.core

An abstract base class for all items which are child items to a BasicItem parent item.

BasicChildItem(D) - 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

BasicItem<D extends BasicData> - Class in net.sf.basedb.core

This is the root superclass of all item classes.

BasicItem(D) - Constructor for class net.sf.basedb.core.BasicItem

Create a new instance.

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.

BasicItemInfo - Class in net.sf.basedb.info

Superclass for all transferable classes that transfer information about item-classes, ie. classes that are subclasses of BasicItem.

BasicItemInfo() - Constructor for class net.sf.basedb.info.BasicItemInfo

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.

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 - Interface in net.sf.basedb.core

The basic interface which all batchers must implement.

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

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.

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.

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(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(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(DbControl) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin

begin(FlatFileParser) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter

Setup error handling and pre-load some of the configuration options.

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(FlatFileParser) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter

begin(DbControl) - Method in class net.sf.basedb.plugins.PackedFileExporter

begin(FlatFileParser) - Method in class net.sf.basedb.plugins.PlateFlatFileImporter

Create a DbControl and a RawDataBatcher.

begin(DbControl) - Method in class net.sf.basedb.plugins.PlateMappingExporter

begin(FlatFileParser) - Method in class net.sf.basedb.plugins.PlateMappingImporter

Save reference to parser.

begin(DbControl) - Method in class net.sf.basedb.plugins.PluginConfigurationExporter

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.

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.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.UnregisterExtensionsProcessor

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.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.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.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(String, AnnotationType, Object, Object, boolean) - Static method in class net.sf.basedb.core.query.Annotations

Create a restriction that searches for annotations between two given values on the root or a joined entity of a query.

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.

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

BfsExporterPlugin.ExtendedExportableField(String, boolean, ExportableField) - Constructor for class net.sf.basedb.plugins.BfsExporterPlugin.ExtendedExportableField

BfsExporterPlugin.ExtendedExportableField(String, String, boolean, ExportableField) - Constructor for class net.sf.basedb.plugins.BfsExporterPlugin.ExtendedExportableField

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

BfsImporter.ProgressEventHandler(ProgressReporter, long) - Constructor for class net.sf.basedb.util.importer.spotdata.BfsImporter.ProgressEventHandler

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, T...) - 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.

bindLimits(String, List<String>) - Method in class net.sf.basedb.core.AbstractSqlQuery

Parse the given SQL and add LIMIT and OFFSET parameters to it.

bins - Variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramSeries

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 - 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.DerivedBioAssayData

bioAssay - Variable in class net.sf.basedb.core.data.RawBioAssayData

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.

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 - 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 - 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.

BioAssaySetClient - Class in net.sf.basedb.ws.client

Web service client for BioAssaySetService in BASE.

BioAssaySetClient(SessionClient) - Constructor for class net.sf.basedb.ws.client.BioAssaySetClient

Creates new BioAssayClient for a session.

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

BioAssaySetInfo - Class in net.sf.basedb.info

Information class for bioassay set in BASE This class holds information that are useful when working with a bioassay set over Web Services.

BioAssaySetInfo() - Constructor for class net.sf.basedb.info.BioAssaySetInfo

Creates a new empty info object

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

BioAssaySetService - Class in net.sf.basedb.ws.server

Web service for BioAssaySet BioAssaySet.

BioAssaySetService() - Constructor for class net.sf.basedb.ws.server.BioAssaySetService

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<D extends BioMaterialData> - Class in net.sf.basedb.core

This is the base class for for the three types of biomaterials: BioSource, Sample and Extract.

BioMaterial(D) - Constructor for class net.sf.basedb.core.BioMaterial

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

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.Type - Enum in net.sf.basedb.core

The type of the event.

BioMaterialEvent.Type(int, String) - Constructor for enum net.sf.basedb.core.BioMaterialEvent.Type

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(boolean) - 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

BioMaterialEventSource.BioMaterialEventSourceTransformer() - Constructor for class net.sf.basedb.core.BioMaterialEventSource.BioMaterialEventSourceTransformer

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

BioMaterialList - Class in net.sf.basedb.core

This class represents a list of biomaterials.

BioMaterialList(BioMaterialListData) - Constructor for class net.sf.basedb.core.BioMaterialList

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

This represents an arbitrary collection of biomaterials.

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

bioMaterials - Variable in class net.sf.basedb.core.data.BioMaterialListData

bioMaterialType - Variable in class net.sf.basedb.core.data.BioPlateTypeData

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 - Variable in class net.sf.basedb.core.data.BioPlateEventParticipantData

bioPlate - Variable in class net.sf.basedb.core.data.BioWellData

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

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

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 - 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

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

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

bioPlateMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter

bioPlateMapper - Variable in class net.sf.basedb.plugins.batchimport.LabeledExtractImporter

Deprecated.

bioPlateMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter

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

bioPlates - Variable in class net.sf.basedb.core.data.BioPlateTypeData

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 - Variable in class net.sf.basedb.core.data.BioPlateData

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

BioSource - Class in net.sf.basedb.core

This class represent biosource items.

BioSource(BioSourceData) - Constructor for class net.sf.basedb.core.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.biomaterial

Collection transformer that given a collection of biosources finds all samples that has the biosources as parents.

BioSourceToSampleTransformer(DbControl) - Constructor for class net.sf.basedb.util.biomaterial.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 - 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 - Variable in class net.sf.basedb.core.data.MeasuredBioMaterialData

BioWell.LockMode - Enum in net.sf.basedb.core

The lock mode for a well is determined by the plate's bio plate type.

BioWell.LockMode(int, String) - Constructor for enum net.sf.basedb.core.BioWell.LockMode

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.LabeledExtractImporter

Deprecated.

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

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.LabeledExtractImporter

Deprecated.

bioWellRowMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter

bioWells - Variable in class net.sf.basedb.core.data.BioPlateData

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

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 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

blueImageFile - Variable in class net.sf.basedb.core.data.SpotImagesData

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.

BOOLEAN - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper

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 in net.sf.basedb.util.formatter

Enum for holding the various types of boolean output.

BooleanFormatter.Type(String, String) - Constructor for enum net.sf.basedb.util.formatter.BooleanFormatter.Type

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

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

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

build - Variable in class net.sf.basedb.info.VersionInfo

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(VirtualDb, VirtualTable, VirtualColumn[], String) - Static method in class net.sf.basedb.core.BatchUtil

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 ...

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.

buildRawMappingSql() - Method in class net.sf.basedb.core.MappingBatcher

Builds the insert SQL statement.

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.

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() - Constructor for class net.sf.basedb.clients.web.taglib.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.table.Button

ButtonAction - Interface in net.sf.basedb.clients.web.extensions.toolbar

Actions represented as buttons in a toolbar.

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 display a clickable button.

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

buttontitle - Variable in class net.sf.basedb.clients.web.taglib.Select

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.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.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.

C

c - Variable in enum net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType

cache - Variable in class net.sf.basedb.clients.web.ExperimentExplorer

The cache of reporter ids matching the current reporter filter.

cache - Variable in class net.sf.basedb.core.hibernate.AbstractQueryCache

cache - Variable in class net.sf.basedb.util.bfs.BaseInputStreamLocator

cache - Variable in class net.sf.basedb.util.overview.cache.NodeCache

cache - Variable in class net.sf.basedb.util.StaticCache.CleanupTask

cacheBase - Variable in class net.sf.basedb.clients.web.servlet.PlotServlet

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

cachedPaths - Variable in class net.sf.basedb.core.Metadata

cachedRssNews - Variable in class net.sf.basedb.clients.web.servlet.RssNewsFeed

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

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.

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

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

calledFrom - Variable in class net.sf.basedb.core.DbControl

To keep track of the code that created this DbControl.

calledFrom - Variable in class net.sf.basedb.util.StaticCache.LockSafeInputStream

calledFrom - Variable in class net.sf.basedb.util.StaticCache.LockSafeOutputStream

canAdd(BioWell) - Method in enum net.sf.basedb.core.BioWell.LockMode

Is it allowed to add (a different) biomaterial to the well?

canAdd(BioWellData) - Method in enum 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

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 net.sf.basedb.core.BioWell.LockMode

Is it allowed to clear a well from biomaterial?

canClear(BioWellData) - Method in enum 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 net.sf.basedb.core.Type

canEnumerate() - Method in enum net.sf.basedb.core.Type

If it makes sense to use values of this type as an enumeration to choose from.

canUseColoring - Variable in enum net.sf.basedb.core.Formula.Type

canUseColoring() - Method in enum 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:

CASE
   WHEN r1 THEN e1
   WHEN r2 THEN e2
   ...
CaseExpression(Expression, WhenStatement...) - 
Constructor for class net.sf.basedb.core.query.CaseExpression
 
caseInsensitive - 
Variable in enum net.sf.basedb.core.FeatureIdentificationMethod
If the feature identifiers may be affect by case sensitivity at the database
                level or not.
caseInsensitive() - 
Method in enum net.sf.basedb.core.FeatureIdentificationMethod
Return TRUE if this identification method can be case insensitive.
caseInsensitive - 
Variable in class net.sf.basedb.core.RawDataBatcher
If case should be ignored when comparing strings (external ID)
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:
                
CASE
WHEN r1 THEN e1
WHEN r2 THEN e2
...
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.TableExistsWork
 
categories - 
Variable in class net.sf.basedb.core.data.AnnotationTypeData
 
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
 
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 - 
Variable in class net.sf.basedb.core.hibernate.SchemaGenerator
 
cfg - 
Static variable in class net.sf.basedb.core.HibernateUtil
The Hibernate configuration, including all mappings.
ch - 
Static variable in class net.sf.basedb.core.ItemContext
 
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
 
chained - 
Variable in class net.sf.basedb.core.Job.ProgressReporterImpl
 
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.
ChangeHistory - Class in net.sf.basedb.core
 
ChangeHistory(ChangeHistoryDetailData) - 
Constructor for class net.sf.basedb.core.ChangeHistory
 
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
 
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 a new URI
                is created were the host:port is replaced.
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.
changes - 
Variable in class net.sf.basedb.core.log.LoggingInterceptor
 
changeType - 
Variable in class net.sf.basedb.core.data.ChangeHistoryDetailData
 
ChangeType - Enum in net.sf.basedb.core.log
Enumeration that representst the type of change that has happened.
ChangeType(int, String) - 
Constructor for enum net.sf.basedb.core.log.ChangeType
 
changeType - 
Variable in class net.sf.basedb.core.log.EntityDetails
 
channel - 
Variable in class net.sf.basedb.core.RawDataProperty
 
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.
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.
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
 
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
 
characterSet - 
Variable in class net.sf.basedb.info.FileInfo
 
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.core.data.FileData
 
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)
charsetParameter(String, String, String) - 
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.
charsetType - 
Static variable in class net.sf.basedb.plugins.util.Parameters
Enumerates all available character sets.
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<?>...) - 
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.
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.
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.
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.
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.
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.
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.
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(Item) - 
Method in class net.sf.basedb.core.BioMaterialList
Checks if the other type is the same type as the member type of
                this list.
checkMemberType(Collection<BioMaterialList>) - 
Method in class net.sf.basedb.core.BioMaterialList
Checks that the lists have the same member type as 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.parser.ColFunction
 
checkNumberOfParameters(int) - 
Method in class net.sf.basedb.util.parser.DataNoFunction
 
checkNumberOfParameters(int) - 
Method in class net.sf.basedb.util.parser.LineNoFunction